[gmx-users] Simulated Annealing command line

[Neena Susan Eappen]

Hi Justin,

Thank you for your answer. I haven't written scripts before, so I was wondering is there a sample script I can see for looping in gromacs.

Thanks,
Neena
________________________________
From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
Sent: Tuesday, January 7, 2020 1:57 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Simulated Annealing command line

Hi Kenny,

Thank you for your answer, but I did not understand clearly. For say 30 cycles of simulated annealing, what I have been doing currently is going through the following steps ( equilibration, annealing, production run, energy minimization) 30 times by changing names of input and output files every cycle.
My question is say after the 1st cycle, is there a way to input a single command line to repeat this process say the remaining 29 times by using energy minimized structure from the end of every cycle as the starting structure for the next cycle.

Any insight would be appreciated,

Thank you,

Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
________________________________
From: Neena Susan Eappen
Sent: Sunday, January 5, 2020 8:43 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [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