[gmx-users] Simulated Annealing command line

[Kenny Goossens]

Hi,

For example, if you name your inputfile system1.gro you can use:
for i in {1..n}; do j=$((i + 1));

followed by your grompp and mdrun commands, using ${i} in the names of your input files and ${j} in the names of your output files.

With kind regards,
______________________________
Kenneth Goossens, PhD student
Laboratory of Medicinal Chemistry (Building A - Room 2.13)
University of Antwerp - Campus Drie Eiken
Universiteitsplein 1
B-2610 Wilrijk
Belgium


________________________________
Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
Verzonden: zondag 5 januari 2020 21:43
Aan: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Onderwerp: [gmx-users] Simulated Annealing command line

Hello gromacs users,

For simulated annealing, I want to repeat cycle (equilibration, annealing, production run, energy minimization) say n times with the energy minimized structure from end of cycle 1 to be used as starting structure for cycle 2. I was wondering is there a way to do this as a loop with just one command line?

Many thanks,

Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
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