The main menu option GROMOS brings you to the menu from which you can run
several GROMOS related commands, ranging from checking the energy of
a structure to starting a full scaleMD run. This WHATIF GROMOS interface
is maintained by Daan van Aalten, which, if you have specific questions,
you can mail at bmb5dva@biovax.leeds.ac.uk
If you are a GROMOS lisence holder, you can get our versions of the GROMOS
source code too. Although they are normally compatible with the official versions,
we sometimes made some clones that give a slightly altered result for some
special purposes. These altered versions will also ONLY be redistributed
to official GROMOS lisence holders.
Be aware that there are several other places where commands can be given
that are somewhat related to the usage of GROMOS.
The menus ANATRA and TRAMOV (see chapter on moleculat dynamics trajectories)
deals with all kinds of options to evaluate molecular
dynamics trajectories. The ESSDYN menu allows you to do essential dynamics
on trajectories.
The second part of this chapter deals with the GROMACS interface
To use GROMOS, WHAT IF requires the following files in the
directory ..../whatif/wregro directory:
Executables Parameter files
PROIONL.EXE IFP37D4.DAT
PROMDL.EXE RT37D.DAT
PROMDL.EXE IFP37C4.DAT
PROMMTL.EXE RT37C.DAT
PROEML.EXE RT37DNEW.DAT
PROGCHL.EXE SPC216.DAT
PROGMTL.EXE SSS.RESLIB
PROGWHL.EXE
PROSDL.EXE
PROBOXL.EXE
PROEMAL.EXE
These files are normally NOT distributed by us, unless you are a
lisenced GROMOS user, and explicitly requested the GROMOS distribution
files to be distributed with WHAT IF.
(READ THIS IF YOU WANT TO USE EM/MD WITHOUT GETTING INTO DETAILS)
If you just want to run a short simple MD run, e.g. to refine a mutant, please
read this and skip the rest of this chapter. Any other experienced GROMOS
user may also be interested in reading this section, because it may
considerably increase the speed at which you can startup your MD runs.
Simply read in your PDB file and type GROMOS to go into the GROMOS
menu. Then type PARAMS to get into the GROMOS parameters menu.
The following flags you may need to change to suit your needs:
STEPS Number of EM steps (default = 5 ps)
HTSTEP Length of your initial MD run (deafult = 5 ps)
MDSTEP Length of your continuation MD run (default = 50 ps)
Then go back to the GROMOS menu by typing END.
There are now three options: FASTEM, FASTHT, FASTMD.
FASTEM does everything to prepare ALL the molecules you have in the
soup for use in GROMOS and then runs an EM run. The resulting
GROMOS coordinate file is called WRE-EMGRO(10).DAT.
FASTHT does the same as FASTEM, but performs a short (see HTSTEP)
MD initilisation run in addition. The atomic trajectories are stored in
WRETRACRD(10).DAT1, the final coordinates in WRE-MDGRO(10).DATxx
where xx is the value of the HTSTEP parameter.
FASTMD does the same as FASTHT, but performs a long continuation
MD run (see MDSTEP) in addition. This MD run is performed in the
background, you quit from WHAT IF when you get the WHAT IF>
prompt back. Trajectory coordinates (WRETRACRD(10).DATxx) and
GROMOS coordinate files (WRE-MDGRO(10).DATxx) are created
every picosecond.
GROMOS was set up with proteins, nucleic acids and sugars in mind. It is
therefore very difficult to make topology files for small molecules (drugs).
The program DAVADRUG was constructed to overcome this difficulty. If you
perform the WREGRO command (see below) to make everything ready for
EM and MD, DAVADRUG is automatically executed to make an accurate
topology for drugs not known by GROMOS which you want to simulate.
During execution of the WREGRO command (see below)
you will be prompted for the number of a drug molecule.
DAVADRUG is executed, reads in the PDB coordinates for the small
drug and uses that as the sole input for the construction of the
drug topology. On the basis of bond-lengths/angles, and a connection
matrix, it determines the SP hybridisation and atom types. You are
then confronted with this initial data via a text editor and you
can make changes as you please. After you quit from the editor,
DAVADRUG starts to determine the GROMOS atom types and adds polar
protons. You can add/delete protons interactively. Then DAVADRUG
calculates all angles, improper dihedrals and dihedrals and
determines the GROMOS types. The drug topology is added as a building
block in the RT37X.DAT file, and you are ready to simulate.
WHAT IF has the possibility to use a special GROMOS derived energy
analyzer to calculate the GROMOS energy per atom. This is not a perfect
option, but sometimes it can be illustrative, or indicative for errors
in a molecule.
In principle you can get these energy terms by running WREGRO followed
by GETETM. If you did run WRUNEM prior
to the GETETM option then
WHAT IF will automatically take the energy minimized structure rather
than the starting configuration.
WHAT IF uses the GROMOS derived program ANALYSE to create a file called
WHAT IF.ANA. This file holds the 9 GROMOS energy terms for each atom.
Internally these nine terms will be added to form the tenth (total energy)
term.
If you run GETETM in a different session from WREGRO, you will be prompted
for the residue range that was given to WREGRO earlier. At present it is
unclear what will happen if you use WREGRO for more than one protein
molecule.
If you want to feed other data to WHAT IF, you can provide a file called
WHAT IF.ANA, with the same format as the real one, and answer WHAT IF's
question `do you want to use the existing energy terms file` with YES.
The command ETPLOT in the GRATWO menu (use %ETPLOT from the GROMOS menu ...)
plots the energy per atom averaged per residue as function of the residue number.
WHAT IF allows you to do all kinds of GROMOS related operations in a somewhat
more user friendly way. The main principle is that as much as possible of
all the files needed for what you want is automatically generated. GROMOS
facilitates too many options to be covered all by WHAT IF. Nevertheless, you
will certainly save many weeks of work thanks to these options. And simple
things like energy minimization on a single protein needs no user interaction
with GROMOS any more.
WHAT IF has a GROMOS preprosessor. The first step is the command WREGRO
WREGRO at present allows only for the creation of topology files
for single stretches of protein, and the possibility to merge protein
topology files, small molecules are allowed as long as
there are standard building blocks available. It is also possible to
setup EM/MD runs in water.
The command WREGRO will cause WHAT IF to prompt you for a residue range and
a pH value. It will then automatically correct for all errors that GROMOS
has in its nomenclature, it will automatically take care of all CYS-CYS
bridges, and it will determine for all protons whether they are present or
absent at the present pH. Subsequently, it will check the hydrogen bonding
potentials of all histidines in the range. The possible donor/acceptorship
of the histidines NE2/ND1 atoms will be displayed and when there are no
contradictions/other difficulties, WHAT IF will automatically make a choice
for you. If WHAT IF cannot find a solution, you will be prompted to make
a choice between a histidine protonated at ND1 or NE2. It is recommended
to check the histidine hydrogen bonds on the screen after WREGRO.
After this, several GROMOS programs are executed, ending up with all
files necessary to start EM/MD.
The GROMOS job/parameter files are generated and presented for editing
depending on the setting of the LEVUSE paramater. If LEVUSE > 0, the
GROMOS input files are presented to the programs GET???.EXE in the whatif
usegro directory,
where ??? can be GMT, GCH, GWH, BOX, ION, -EM, or -MD. These programs
(written by D.M.F. van Aalten, 10-'93) convert the parameter files to
a human readable format. These files are then pulled up in your favourite
editor (defined in dbdata/CCONFI.FIG). All the
parameters are listed together
with their meaning as described in the GROMOS manuals. You can edit the
parameters if you want and after you saved the files and quit from your editor,
the program PUT???.EXE convert the file you edited back to GROMOS parameter
files. Depending on the setting of LEVUSE, the files WREJOB???.COM and
WREINP???.DAT (the job and parameter file respectively) will be subsequently
pulled up in your editor for editing. If you are not an experienced user,
do not edit these files.
WHAT IF will generate the PROGMT job file called WREJOBGMT.COM, the input
parameters are stored in WREINPGMT.DAT. PROGMTL.EXE will then be
executed interactively. The resulting file WREMTD.BIN will contain the
binary GROMOS topology of your system.
Thereafter the GROMOS coordinate file will be written. The 'corrections'
needed for GROMOS (ILE CD1 -> ILE CD; VAL CG1 and CG2 swapped; LEU CG1 and
CG2 swapped) will be performed. The N- and C-terminus will be modified to
NH3 and COO respectively
At this stage, if there are drugs in the selected range, WHAT IF will ask
you some questions on how to incorporate them in the topology file.
You can add any drug you want if it is described in the RT37D.DAT files
with the only limitation that you should take care of the fact that the
atom sequence of the drug in the RT37D.DAT file and the soup (= coordinate
file you read in) is identical.
If the drug is not in the RT37D.DAT file, WHAT IF will automatically
call PRODRG unless you already have a drug topology file which is merged
to the main protein topology file later.
Also, if USEWAT > 0, WHAT IF will aks you for the range of
crystallographic water molecules
you want to incorporate in the EM/MD run.
Then, WHAT IF will generate the job file called WREJOBGCH.COM and the
parameter file WREINPGCH.DAT needed to run PROGCH. Since hydrogen atoms are
not generally listed in PDB files, GROMOS adds them to the coordinate file
using PROGCH. PROGCHL.EXE is also run interactively.
THE FOLLOWING WILL ONLY HAPPEN IF THE PARAMETER USEWAT > 0
If you also requested to use the waters present in the soup in your EM/MD
run, WHAT IF will create a job file called WREJOBGWH.COM and the
parameter file WREINPGWH.DAT needed to run PROGWH. Hydrogen atoms of
water molecules are also not stores in PDB files (and the soup), so
PROGWH is used to add H-atoms to the water oxygens. PROGWH.EXE is run
interactively.
THE FOLLOWING WILL ONLY HAPPEN IF THE PARAMETER USEWAT > 1
If you requested periodic boundary conditions (fill a large box
with your protein in it with water), WHAT IF creates the job file WREJOBBOX.COM
and the parameter file WREINPBOX.DAT for PROBOX. PROBOXL.EXE is run interactively
and the number of generated water molecules plus the dimensions of your box
will be shown upon termination.
THE FOLLOWING WILL ONLY HAPPEN IF THE TOTAL CHARGE OF YOUR SYSTEM IS NOT ZERO
Immediately after your topology was built (see above), WHAT IF calculates the
total charge of your system. If this is not equal to zero, WHAT IF will create
a job file WREJOBION.COM and a parameter file WREINPION.DAT
Because you added ions to your system, they also have to be included in
the topology, so the job file WREJOBGM2.COM and the parameter file WREINPGM2.DAT.
Again, PROGMTL.EXE is run.
At the end of the WREGRO run, you will find a couple of files in your directory:
WGRWPR.GRO The first, hydrogen-, drug- and waterless coordinate file
WGRGMT.INP Parameter file for PROGMT
WGRGMT.SCR Job file for PROGMTL.EXE
WGRGMT.OUT The output from PROGMT
WGRGMT.TOP The binary topology file
WGRGCH.INP Parameter file for PROGCH
WGRGCH.SCR Job file for PROGCHL.EXE
WGRGCH.OUT The output from PROGCH
WGRGCH.GRO The coordinate file including drugs and hydrogens
IF USEWAT > 0 :
WGRGWH.INP Parameter file for PROGCH
WGRGWH.SCR Job file for PROGWH.EXE
WGRGWH.OUT The output from PROGWH
WREWATGRO.DAT Coordinate file of water oxygens without hydrogens
^^^^^^^^^^^^^ That name changed to ....?
WGRGWH.GRO Coordinate file of water oxygens with hydrogens
IF USEWAT > 1 :
WGRBOX.INP Parameter file for PROBOX
WGRBOX.SCR Job file for PROBOXL.EXE
WGRBOX.OUT The output from PROBOX
WGRBOX.GRO Coordinate file containing protein, drugs, water
IF USEWAT > 1 AND TOPOLOGY NOT NEUTRAL :
WGRION.INP Parameter file for PROION
WGRION.SCR Job file for PROIONL.EXE
WGRION.OUT The output from PROION
IF USWAT > 1 AND TOPOLOGY NOT NEUTRAL :
WGRGM2.INP Parameter file for PROGMT
WGRGM2.SCR Job file for PROGM2L.EXE (identical copy of PROGMTL.EXE)
WGRGM2.OUT The output from PROGMT
WGRGM2.TOP The binary topology file (overwrites previous version)
IN all cases there is also WRETWOGRO.DAT, which is used as input for EM/MD.
Be aware that the project number is coded in all these files.
In case you do not do too complex things, you can
immediately use the command WRUNEM
to do a GROMOS energy minimalisation run. If you type WRUNEM,
WHAT IF just generates the job file WREJOB-EM.COM
and the parameter file WREINP-EM.DAT. This file is pulled up in your
favourite editor after conversion to human readable format by the program
GET-EM. After you quit from editing, WHAT IF then executes PROEML.EXE
to perform the EM run. WHAT IF expects that the file WREMTD.BIN is the topology
file, and WRETWOGRO.DAT is the coordinate file. Also, WHAT IF expects that the
parameters are already set correctly for this run. (See command PARAMS).
After the run you will find a few files in your directory:
WREGRO-EM.DAT Formatted GROMOS coordinate file after minimalisation.
WREOUT-EM.LIS Formatted (descriptive) output from this EM run.
WRE-MDGRO.DAT0 Copy of WRE-EMGRO.DAT for administrative reasons.
These file names might be different depending on the parameters (see PARAMS).
See WRUNMD.
You can use the commands HEATUP/WRUNMD to do a special startup of
a GROMOS molecular dynamis run. If you type HEATUP,
WHAT IF just generates the job files WREJOB-MD.COM
and the parameter files WREINP-MD.DAT. Only the first file is pulled up in your
favourite editor after conversion to human readable format by the program
GET-MD. After you quit from editing, WHAT IF then executes PROMDL.EXE
to perform the MD run. In this run, the temperature is slowly increased,
the temperature/pressure coupling constant slowly increased as well as the
CUTOFF radius. This results in a slow increase of forces, preventing
a crash of SHAKE. If you just want to perform a short MD run, this is
also a good option. If WRUNMD is used, the simulation is initiated using
velocities chosen from a Maxwellian distribution at the selected temperature.
WHAT IF expects that the file WREMTD.BIN is the topology
file, and WRE-MDGRO.DAT0 is the coordinate file. Also, WHAT IF expects that the
parameters are already set correctly for this run. (See command PARAMS).
After the run you will find a few files in your directory:
WREGRO-MD.DATXX Coordinate file (largest XX = the final one).
WREOUT-MD.LISXX Formatted (descriptive) outputs from the HEATUP run.
WREINP-MD.DATXX PROMDL input files
WREINP-MD10.COM_CONT PROMDL input file for the continuation MD run
Trajectory files are also written, see CONTMD
XX = file identification number for each picosecond in HEATUP.
If you have performed a startup run using HEATUP or WRUNMD, you are ready to
perform a so-called MD continuation run, generating a long trajectory which you
can analyse later. The MD run is executed from a script (WREJOB-MD.COM_CONT)
one picosecond at a time. This is convenient, when you run out of
diskspace or your machine crashes, you can only loose a maximum of 1 ps on
CPU time. The MDSTEP parameter (see PARAMS) determines how long your MD
run is. If you type CONTMD, WHAT IF looks in your directory for the LAST
WRE-MDGRO.DATxx file and continues your simulation from there.
After the run you will find a few files in your directory:
WREGRO-MD.DATxx Formatted GROMOS coordinate file after each ps of MD.
WREOUT-MD.LISxx Formatted (descriptive) output of each ps of MD.
WRETRACRD.DATxx Coordinates trajectory file of each ps of MD.
WRETRAVEL.DATxx Velocities trajectory file of each ps of MD.
WRETRAENE.DATxx Energies trajectory file of each ps of MD.
Often one is rather certain about the fold, but not at all about the
total structure. This is especially the case after building by homology
from a structure with a high homology, or after making a few point mutants.
In those cases it is wise to do the MD and/or EM with the alpha carbons
fixed. There is no direct option to do this, but one can set the parameter
FIXCAS in the PAREMD menu to switch alpha carbon fixing on. The parameter
FIXFRC then determines the force used by GROMOS to hold the alpha carbons
in place. The maximum force allowed (at present) is 32000. This normally keeps
the alpha carbons in long MD runs within 0.2 Angstrom of their original
position, unless your structure is extremely bad.
All GROMOS programs create a user readable output file with results and the
flow of the program in it. Also in case of errors, the error messages are
written in this file. All these files have the extension .LIS. See one of
the appendices for a complete list of default file names used by WHAT IF.
You can use the following commands to get these files in the editor
at the screen:
(of course you can also just type, edit or print them by hand)
The command SHOGMT will cause WHAT IF to bring the formatted user readable
log file of the last PROGMT run in the editor. You can of course also type,
edit, or print this output file by hand. See the appendices for a list
of GROMOS related default file names used by WHAT IF.
The command SHOGCH will cause WHAT IF to bring the formatted user readable
log file of the last PROGCH run in the editor. You can of course also type,
edit, or print this output file by hand. See the appendices for a list
of GROMOS related default file names used by WHAT IF.
The command SHOGWH will cause WHAT IF to bring the formatted user readable
log file of the last PROGWH run in the editor. You can of course also type,
edit, or print this output file by hand. See the appendices for a list
of GROMOS related default file names used by WHAT IF.
The command SHO-EM will cause WHAT IF to bring the formatted user readable
log file of the last PROEM run in the editor. You can of course also type,
edit, or print this output file by hand. See the appendices for a list
of GROMOS related default file names used by WHAT IF.
The command SHOMD will cause WHAT IF to bring the formatted user readable
log file of the last PROMD run in the editor. You can of course also type,
edit, or print this output file by hand. See the appendices for a list
of GROMOS related default file names used by WHAT IF.
The command SHOMMT will cause WHAT IF to bring the formatted user readable
log file of the last PROMMT run in the editor. You can of course also type,
edit, or print this output file by hand. See the appendices for a list
of GROMOS related default file names used by WHAT IF.
The command SHOBOX will cause WHAT IF to bring the formatted user readable
log file of the PROBOX run in the editor. You can of course also type,
edit, or print this output file by hand. See the appendices for a list
of GROMOS related default file names used by WHAT IF.
The command SHOION will cause WHAT IF to bring the formatted user readable
log file of the PROION run in the editor. You can of course also type,
edit, or print this output file by hand. See the appendices for a list
of GROMOS related default file names used by WHAT IF.
The command EDITOP first converts the binary GROMOS topology file
(WGRGMT.TOP) to ASCII format. This ASCII file is then pulled into
your favourite editor for manual adjustments. After saving a new
binary topology file is generated.
The command ENERAN joins WGR-MD.ETR* files allowing you to view
several GROMOS energies as a function of time.
Writes molecules in the soup into a GROMOS style coordinate file.
Merges two binary topology files. Used with care, this is a way
to be able to simulate more than 1 protein chain with GROMOS.
The several WHAT IF - GROMOS preprocessor related options have their own
parameter
menus available. This chapter give a short description of the parameters that
can be changed in order to influenze the behaviour of the program.
The command PARAMS brings you to the menu from which you can change the
parameters for GROMOS. You can change the following
parameters:
This parameter determines the flow of the WREGRO option: Just create decks?
Edit all decks? Run them when ready? When LEVBUSE > 0, the programs
GET???.EXE and PUT???.EXE are used to cycle between unreadable GROMOS
parameter files and human readdable format. The following values are allowed:
0 : Create all files, don`t edit them, run them.
1 : Create all files, edit parameter files only, then run them.
2 : Create all files, edit parameter/job files, then run them
Determines the way the minimization steps are determined. Steepest descent
or conjugate gradient.
1 : Steepest descent
2 : Conjugate gradient
Allows choice between gradual heating and normal MD heatup
This parameter determines the maximal number of steps. If the minimization
is completed before this number of steps is reached, minimization is
also stopped. STEPS can range from 1 till 500.
In case you use the conjugate gradient method for minimization, this
parameter determines after how many steps a new gradient correction will
be performed. NEWGRD can range from 1 till 10.
This parameter determines whether the bond lengths are constrained or not.
0 : Do NOT use SHAKE.
1 : Use SHAKE for hydrogens only
2 : Use SHAKE for all bonds
The minimization stops as soon as the energy difference between two consequetive
steps is less than MINDIF. MINDIF can range from 0.001 till 1.0.
This is the step size (only in case you use steepest descent?) with which the
minimization starts. This stepsize will be updated during the minimization.
STPSIZ may range from 0.001 till 0.05.
The stepsize during the minimization procedure (only in case of steepest
descent?) is continuously automatically being updated. However, the step
size is not allowed to exceed MAXSTP. MAXSTP may range from 0.01 till 0.1.
XTC is a special compressed format with is 4 times better than UNIX compress on
normal GROMOS trajectory files. It is used by default but here you can turn it off.
Hydrogens can be placed either by a GROMOS routine (PROGCH) which uses
a simple geometrical approach, or with the HB2 module which searches
through several possibilities to find an optimum.
This parameter determines whether alpha carbons will be forced towards
their original position or not. This parameter must be set before the
WREGRO option is executed.
0 : Don't fix alpha carbons.
1 : Do fix alpha carbons.
This parameter determines the force with which alpha carbons are held in place.
See the GROMOS writeup for a description. Normal values are 1000 till 32000.
This parameter determines in the length of your initiation MD run
(see HEATUP/WRUNMD). Default is 5, use HEATUP and HTSTEP=25
for a realy gentle (but slow) heatup of your system.
This parameter determines the number of ps in the continuation MD-run. (1-10000).
This parameter determines the temperature during an MD-run (1.0-999.9).
Determines pairlist generation cutoff distance. Choose 8 or higher.
Long range electrostatic cutoff.
This is the maximal deviation from the temperature set with the TEMP
parameter. If the average temperature differs more, temperature rescaling
will be performed.
This parameter determines whether trajectories are written out during an
MD run or not. Trajectories are always written unformatted.
the allowed values are:
0 : do not write any trajectories to file (default)
1 : only write the coordinate trajectories to file
2 : write the coordinates and the velocities to file
3 : write coordinate, velocity and energy trajectories
Coordinate trajectories are written in the file WRETRACRD.DAT. Velocity
trajectories are written in the file WRETRAVEL.DAT. Energy trajectories
are written in the file WRETRAENE.DAT.
At present WHAT IF can only follow up with coordinate trajectory movies.
Allows you to specify the number of timeframes to skip each time before writing
a timeframe to the trajectory file.
This paragraph holds some GROMOS related WHAT IF options that were hard to
place in any category.
If you want to run torsion EM or MD with torsion angle restraints, you
have to add one card for every angle to the input deck for PROEM or PROMD.
The command TRSFIL creates a file with the correct format, but more important
also the correct atom numbers (!!), for all phi, psi, and omega angles in
a range of residues.
You will need to have the molecule you want to use this option on in the
soup. You also need to have this same molecule as a GROMOS coordinate
file. WHAT IF needs this to make a correspondence between the GROMOS
atom order and the IUPAC atom order. You will be prompted for the GROMOS
file, the number of the corresponding molecule in the soup, the range
of residues in this molecule for which you want to get the restraint
cards created, and the name of the restraint file. You will also be prompted
for three force constants. These are the force constants for phi, psi,
and omega respectively. The last two parameters on the restraint card are
just arbitrary set to some numbers which allow for easy editting.
When WHAT IF activates PROGMT, it only allows for the usage of one protein
chain, and the following drugs:
GROMOS
name number description
HEME 41 heme group (charge-2, acidic groups deprotonated)
FMNO 42 flavin mononucleotide (oxidized, deprotonated at
FN5 and FN1; charge-1 OPOHO2-)
FMNS 43
etc. see GROMOS writeup
MTH 83 methanol (neutral)
H2O 82 water (neutral)
SO4 68 SO4 ion (charge-2)
ZN 76 zinc (charge+2)
NA 77 sodium (charge+1)
CL 78 chloride (charge-1)
CA 79 calcium (charge+2)
MG 80 magnesium (charge+2)
Other groups can be generated automatically with DAVADRUG during WREGRO.
WHAT IF assumes that both the N-terminus and the C-terminus are not blocked.
That means the N-terminus automatically gets three H-atoms and the C-terminus
an O-atom attached to it. Of course you can change this during WREGRO.
There are several ways of working with coordinate files etc (formatted or
unformatted in all kinds of combinations). WHAT IF has chosen one of these
combinations, and uses that one systematically (formatted).
It is NOT possible (yet) to use more than one peptide chain in a GROMOS run.
Besides GROMOS, WHAT IF can also use the services of the GROMACS molecular
dynamics program. In this preliminary version of the PREGMX interface there are
a few limitations. First, small (non-protein) molecules cannot be included in the
simulation. Second, multiple protein chains are not supported. FInally, the present
verion of GROMACS does not properly support DNA molecules. For all the options
several parameters can be adjusted in the GMXPAR menu.
The first step in GROMACS, as with many other MD programs is to create a topology file
of the system. A range from the soup is selected, and a PDB file is written which is
then used as input for the PDB --> topology converter of the GROMACS suite. Hydrogen
atoms are added where necessary, and the final GROMACS coordinate file ends up in
gmx.gro
In addition to MAKTPB, the protein is placed in a box of water molecules resulting in
the file box.gro. If
necessary, waters are substituted for ions to ensure electrostatic neutrality. The
file with both water molecules and ions is ion.gro.
After having created a solvated system with MAXBOX, we can now actually 'do' something.
GMXFEM automatically runs MAKTPB/MAKBOX and then starts an energy minimisation.
The energy minimized coordinates end up in em_.gro.
In order to start a long MD run, a short startup run is normally performed first.
By default, a 5 ps MD run is performed, taking velocities from a Maxwellian
distribution at 300 K. Position restraints are used to optimize protein - water
interactions.
Having finished the startup run we are now ready for the big work. GMXFMD does
everything for you automatically, from MAKTPB to a continuation MD. The long MD run
is submitted in the background, so you get the WHATIF> prompt back immediately.
Cut-off distance used when making the pairlist.
Cut-off used when calculating long range electrostatic interactions.
Determines the length of the EM run
Determines the length of the MD startup run.
Determines the length of the MD continuation run.
GROMACS data, like energies, velocities etc. are written with a certain frequency.
Usually, one can reduce diskusage considerably by changing this parameter.
GROMACS writes its trajectories in the highly compressed and portable XTC format.
With this parameter you determine how often frames are written.
The size of the box generated depends on the largest distance between any pair of
atoms in the system. Thus, if your coordinate file contains crystallographic waters
this may cause a too large box to be generated. DELH2O takes care of that by
removing remote water molecules.
BOXDIS basically determines how big your box is going to be with a given protein.
Care should be taken that (although this is checked by the WHATIF PREGMX interface)
protein atoms cannot 'feel' each other through the periodic boundary conditions.
This can be prevented by choosing a BOXDIS which is significantly larger than
0.5 * CUTOF1
FASTMD allows one to setup a long GROMACS run with just 1 command. More advanced
GROMACS users might desire a more interactive environment, which can be set with the
INTLEV flag.
During MD it is sometimes desirable to restrain the positions of
a selection of atoms. FIXPAR determines which atoms should be
restrained and when.
0 = all atoms restrained only during initial MD startup run
1 = all atoms restrained at any time
2 = only CA atoms restrained at any time
3 = restraints defined manually, by reading the file posre.itp
Determines how tight the atoms should be restrained to their positions.
Allows specification of an external distance restraints file
0 = do not use distance restraints
1 = include the distance restraints in the file disre.itp
0 = run in vacuum
1 = cubic box