Re: [AMBER] TIP3 simulated annealing, 200ps*50 loops = 10ns ==> Minimization of lower energy structures

From: Carlos Simmerling <>
Date: Sun, 20 Dec 2015 09:44:15 -0500

I'm not sure I understand. If your goal is to minimize the final structure
from md, use the final rst file as the inpcrd. If the goal is to minimize
the low energy snapshots,use those as inpcrd. I don't think energy analysis
of snapshots in explicit water is very meaningful though. The water
introduces significant noise to the snapshot energies. In any case,the same
prmtop can be used for all snapshots.
On Dec 20, 2015 7:23 AM, "V. Kumar" <> wrote:

> Dear AMBERist
> I planing to perform minimization after simulated annealing ( 200ps*50
> loops = 10ns). Visual inspection of my low energy structures extracted from
> trajectory shows that there are still some strains on the side chains. I
> already performed minimization that removed the strain. But I am not sure
> that I did it in correct way (protocol).
> I have 50 sets(loops) of 200 ps simulated annealing MD data in explicit
> solvent using NMR restraints during simulation. As per the low energy
> search I found 10 structures from the different "md" sets. For eg. I have
> md1, md2, md3, ...md50. I picked low energy structures lets say from md34,
> md47, md50, few more.
> Now my question is I have same ".prmtop" for all strucuture, but I have
> different ".rst" files. For eg. md1.rst, md2.rst, ......md50.rst. So to
> minimize above 10 structure, for each model I constructed again new
> ".prmtop and .inpcrd" and then I performed minimization in usual way. I
> dont know its a correct way to do it.
> I also got another idea to use same prmtop but respective rst files to
> minimize all 10 structures. I clearly dont know which method is correct. So
> kindly request your suggestion and comments.
> thanks in advance..
> Have a nice weekend
> Best wishes
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Received on Sun Dec 20 2015 - 07:00:03 PST
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