Index of /examples/chemistry/basic

[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory   -  
[ ]conf.pdb 2019-08-28 10:20 526  
[TXT]edsam_reference.xvg 2019-08-28 10:20 3.5K 
[ ]eigenvec.trr 2019-08-28 10:20 840  
[ ]grompp.mdp 2019-08-28 10:20 11K 
[ ]mdout.mdp 2019-08-28 10:44 11K 
[ ]out.gro 2019-08-28 10:45 228  
[ ]sam_reference.edi 2019-08-28 10:20 1.0K 
[ ]sample.cpt 2019-08-28 10:48 1.0K 
[SND]sample.edr 2019-08-28 10:48 2.0K 
[ ]sample.gro 2019-08-28 10:48 324  
[TXT]sample.log 2019-08-28 10:48 21K 
[ ]sample.tpr 2019-08-28 10:44 2.6K 
[ ]sample.xtc 2019-08-28 10:48 624  
[TXT]submit.sub 2019-08-28 10:51 453  
[ ]topol.top 2019-08-28 10:20 1.4K 

RCS sample computational chemistry jobs

Sample Gromacs scripts

This directory contains a simple Gromacs MD simulation scripts.

Available gromacs modules:

Select the version of Gromacs:
scc1% module avail gromacs
gromacs/2016.3 gromacs/2018.3 gromacs/2019.1 gromacs/2019.1_openmpi_3.1.4

Load the selected version of Gromacs:

scc1% module load openmpi/3.1.4
scc1% module load cuda/9.2
scc1% module load gromacs/2019.1_openmpi_3.1.4

Submit Gromacs job using Batch:

This directory contains a simple submit.sub script that, when submitted to the batch system, will execute the Gromacs scripts in the same folder.
To submit the job, type the following command at the SCC prompt:
scc1% qsub submit.sub

Helpful Links:

Running Jobs on the SCC