[gmx-users] Potential energy

[Justin Lemkul]

On 12/28/13, 2:12 AM, Ali Alizadeh wrote:
> Dear Justin,
>
> Thank you very much for your reply.
>
> One point, why useless??? You meant this potential calculation is useless?
>

It's useless because no force field has been derived to reproduce such a value. 
  "The potential energy of a molecule" is useless outside the context of a given 
force field, and since none of those force fields was designed to generate 
meaningful values there, it serves no useful purpose.  Some force fields have 
been parametrized to reproduce QM interaction energies, hence why pairwise 
interaction energy is a potentially informative value.

-Justin

>
> On Sat, Dec 28, 2013 at 2:30 AM, Ali Alizadeh <ali.alizadehmojarad at gmail.com
>> wrote:
>
>>
>> Dear All users,
>>
>> I have a question about calculation of potential energy for an especial
>> group. I know I had to
>>
>> define an energy group in .mdp file. I forgot to do it. I want to know can
>> I extract this potential
>>
>> energy by post processing or not? If not this means I must perform my
>> simulation again?
>>
>>
>> --
>> Sincerely
>>
>> Ali Alizadeh
>>
>> Justin wrote:
>
> There is no .mdp option to calculate the potential energy of just a single
> group.  One can excluded nonbonded interactions between pairs of groups or
> decompose nonbonded energy between pairs of groups.
>
> One could obtain "the potential energy of a group" by stripping out the
> coordinates of interest from the original trajectory (with trjconv), making a
> matching .tpr file (with tpbconv), then recalculating energies with mdrun
> -rerun.  Such a quantity would be useless, though.
>
>
>

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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