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

From: V. Kumar <vin.vasanth.gmail.com>
Date: Sun, 20 Dec 2015 13:23:27 +0100

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
AMBER mailing list
Received on Sun Dec 20 2015 - 04:30:03 PST
Custom Search