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GROMACS

 • General information

 • How to use

      • Examples

 • Jobs Monitoring

 • More information

General information

2018 version. GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

How to use

send_gmx

To send gromacs to the queue system  use the send_gmx utility. When executed, shows the command syntax, which is summarized below:

send_gmx ``JOB and Options'' NODES PROCS_PER_NODE TIME MEM [``Other queue options'']
``JOB and Options'': options for the calculation and input of GROMACS name extension. It is very important to keep the quotes.
NODES: Number of nodes.
PROCS: Number of  processors.
TIME: Time requested to the queue system, format hh:mm:ss.
MEM: Memory in Gb.
[``Otras opciones de Torque'' ] There is the possibility to pass more variables to the queuing system.
See examples below.   More information about this options

Examples

We send the gromacs input job1 to 1 node, 4 processors on that node, with a requested time of 4 hours and 1 GB of RAM:

send_gmx ``-s job1.tpr'' 1 4 04:00:00 1

We send job2  to 2 compuation nodes, 8 processors on each node, with a requested time of 192 hours, 8 GB of RAM and to start running after work 1234.arinab is finished:

send_gmx ``-s job2.tpr'' 2 8 192:00:00 8 ``-W depend=afterany:1234'

We  send the input job3 to 4 nodes and 4 processors on each node, with a requested time of 200:00:00 hours, 2 GB of RAM and we request to be send an email at the  beginning and end of the calculation to the direction specified.

send_gmx ``-s  job.tpr'' 4 4 200:00:00 2 ``-m be -M mi.email@ehu.es''

send_gmx command copies the contents of the directory from which the job is sent to /scratch or /gscratch, if we use 2 or more nodes. And there is where the calculation is done.

Jobs Monitoring

To facilitate monitoring and/or control of the gromacs calculations, you can use remote_vi which shows the md.log file (only if it was sent using send_gmx).

More information

http://www.gromacs.org/About_Gromacs

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