[gmx-users] Simulated Annealing command line

[Justin Lemkul]

On 1/7/20 8:57 AM, Neena Susan Eappen wrote:
> 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.

It's not a "single command" per se, but it's easy to do this in a 
for-loop in a shell script. As Kenny pointed out, you have two counters, 
i and j, which specify the index of the file to be used. If j=i+1, then 
for cycle $j, you use the coordinates, checkpoint, etc. of cycle $i as 
input to grompp, and then execute mdrun.

-Justin

> 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

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Justin A. Lemkul, Ph.D.
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