Informazio orokorra
2018 bertsioa. 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.
Nola erabili
send_gmx
GROMACS lanak kolara bidalzeko send_gmx tresna sortu dugu. Egikaritzerakona, aginduaren laguntza erakusten da. Erabiltzeko modua:
send_gmx ``JOB and Options'' NODES PROCS_PER_NODE TIME MEM [``Other queue options'' ]
| ``JOB and Options'': | Kalkuluaren opzioak eta inputaren izena (extensioarekin). Oso garrantzitsua da komilla arten jartzea. |
| NODES: | Nodo kopurua. |
| PROCS: | Prozesagailu kopurua. |
| TIME: | kolari eskatutako denbora hh:mm:ss. formatuan |
| MEM: | memoria en Gb-etan. |
| [``Torque beste aukerak'' ] | kola sistemari agindu gehiago pasatzeko modua. Ikus beheko adibideak[intlink id=”632″ type=”post”]. informazio gehiago[/intlink] |
Adibideak
send_gmx ``-s job1.tpr'' 1 4 04:00:00 1 send_gmx ``-s job2.tpr'' 2 8 192:00:00 8 ``-W depend=afterany:1234'' send_gmx ``-s job.tpr'' 1 8 200:00:00 2 ``-m be -M mi.email@ehu.es''
Ohiko pbs script bat sortu eta hau ere bidlai daiteke gero kolara. send_gmx erabili dezakezue adibide bat sortzeko.
Kalkuluen monitorizazioa
remote_vi erabiliz md.log fitxeroa ikutsiko dugu.