[gmx-users] Re; calculating interaction energies of dimers and ligand

[Justin Lemkul]

On 2/16/15 12:03 AM, RJ wrote:
> Dear Justin,
>
>
> I notice that -rerun option in mdrun.
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> As per your suggestion, i have made a tpr file using energyrps in md.mdp file as like this
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> gmx grompp -f md.mdp -c npt.gro -t npt.cpt -o check.tpr
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> and tried to use mdrun -reun
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> gmx mdrun -rerun check
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> but end up with
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> Can not open file:
> topol.tpr
>

Right, because mdrun always needs instructions for what to actually do.  You 
make a new .tpr file with whatever groups you want for interaction energy, and 
use mdrun -rerun to calculate those quantities.

-Justin

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> Dear Justin,
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> I already ran 10 ns without mentioned the energyrps. Now I have added the energyrps in md.mdp file. Should i need to rerun 10 ns again to get the interaction energies?
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> what does mdrun -rerun ?
> On 2/13/15 7:07 AM, RJ wrote:
>> Dear all,
>>
>>
>> I need to calculate the interaction energy (Column SR & LJ SR) of chain A with chain B.
>>
>>
>> Should I need to select the specific interacting residues to between chain A and B ? Also to chain C ( Ligand molecule)?. I used the gmx energy command line but there are index.ndx option to indicate the group of residues so?
>>
>
> To get this information printed to the .edr file, you need to do your run with
> correct energygrps defined. If you didn't do that, create a .tpr file that
> specifies these groups and re-calculate energies with mdrun -rerun.
>
>>
>> Also, how do i calculate the interaction energies in nano second time scale ( seems there is no -tu option in gmx energy)?
>>
>
> Just convert after the fact in the text file or plotting software. The time
> unit is always ps in .edr files.
>
> -Justin
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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