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3 LaunchGromacs

launch

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Mireia Segado
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26 views4 pages

3 LaunchGromacs

launch

Uploaded by

Mireia Segado
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as DOCX, PDF, TXT or read online on Scribd
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How to run classical molecular dynamics simulations in GROMACS

In KIMIK2, you will find a folder named /home/cbgshared.

There, find the MD/files folder containing all example files and scripts you will need.

In order to launch gromacs calculation you need the following files in the folders, firstly we
enummerate the files and later on we explain where to find these files or how to generate them.

1. List of Files and Folders:

MAIN FOLDER :

 Name of main folder:

e.g. /home/msegado/GROMACS/LIN24_CS48_SOL25415/

$mainfoldername= LIN24_CS48_SOL25415

 Files inside Main folder:

$mainfoldername.gro coordinate file of whole system


$mainfoldername.top topology file (number of molecules of each type
and llinks to all the force fields use for them)

ffnonbonded.itp All non bonded parameters


forcefield.itp link to general force fields used and definition
of coulombic and lennard jones interaction
If monoatomic cations are in solutions eg: Cs, Mg, .. this additional files is needed:

cations.itp Type of chosen force field for cation


SUBFOLDERS :

 Folders inside main folder with MD simulations: e.g. NVT, NPT, MINIM
 Files inside subfolder for MD simulations:

name.mdp run input of MD simulation; all MD details.


job file launch calculations
2. Find or Generate Files:

.gro file Generation explained in tutorial 1_Box_Generation


cation.itp you have to copy this file from
/home/msegado/GROMACS/GROMACS_INFO/ForceFields_Mireia/ions/
and modify it with the cations forcefield chosen. (more explanation in
ions subfolder).
forcefield.itp you select the forcefield opls and charmm that would like to use and
copy from
/home/msegado/GROMACS/GROMACS_INFO/ForceFields_Mireia/ the
force field selected.
* forcefield_cr2.itp combination rule 2 of lorentz
.top Groups have to be renamed in .top file
Number of molecules has to be modified
ffnonbonded_lalala.it you select the forcefield opls and charmm that would like to use and
p insert in ffnonbonded the parameters file.
Insert at the end of the file the ffnonbonded of the molecules selected of
e.g POM or molecules or cations if they are not defined. Copy
ffnonbonded for the molecule from
/home/msegado/GROMACS/GROMACS_INFO/ForceFields_Mireia/molec
ules and insert /ions/ffnonbonded_cations.itp new parameters for alkali
cations.
rename ffnonbonded with e.g ffnonbonded_LIN24_CS48_SOL25415.itp
IMPORTANT:
ONLY ONE ffnonbonded.itp file must be.
Files that are redirected forcefield.itp file that are in external folder in cbgshared:

ffbonded_molecu For bonded parameters different molecule.itp (where geometry and bonds
le.itp
are defined) could be included.
the ffbonded parameters are in
/home/msegado/GROMACS/GROMACS_INFO/ForceFields_Mireia/molecules;
Link in topology file ffbonded.itp files of the molecules that appear in MD.
!take care that for each molecule with have fixed frozen position and free
positions.
Ffbonded.itp you select the forcefield opls and charmm that would like to use and insert in
ffnonbonded the parameters file.

In the subfolders MINIM, NVT and NPT you will find examples of .mdp and job files:

JOB FILE:

Specification of The jobs are prepared to launch in machine with


cues
maxium of processors in our case 24 processors and 4
GPU. Then you launch Stage I, II and III. At the same
time and when one step is finished the next calculations
enters.

Load Module
Create .tpr file generated in nonhuman language by comination of
top;gro and mdp run, which gromacs uses to launch
calculation)

Launch .tpr

Folders have to be renamed in run job.

Groups have to be renamed in .mdp examples.

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