[gmx-users] Energy cal from MD simulations

[Justin Lemkul]

On 1/12/19 1:10 AM, Lod King wrote:
> Hi,
>
> I have obtained a 100 ns simulation using Amber. I would like to calculate
> the potential energy (VDW, COUL,ect) from the trajectory, below is my
> command.
>
> $gmx grompp -f test.mdp -p ../gromacs.top -n ../index.ndx -c ../300.pdb -o
> rerun.tpr -maxwarn 1

It is always dangerous (and usually wrong) to ever use -maxwarn.

> $gmx mdrun -rerun ../protein.trr -s rerun.tpr -g rerun.log -e rerun.edr
>
> $gmx energy -f rerun.edr -o test.xvg
>
> My question is: in this test.mdp file, should I specify any parameters that
> should be the same as I used when running MD using Amber.

If you're looking to obtain an equivalent output, yes.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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