[15-XI-2012]
Thank you very much for your help Dr. Case,
I did the test you suggest me (comparing the 1-step MD with the imin=5) last friday for a small in-vacuo system with 20000 snapshots and I obtained the same values, but I posted the question just to be sure that, from a computational point of view, the implementation was OK in both cases.
Anyway, I still have to compare the results with a NVT explicit solvent to be sure that everything is OK also in that case.
Kepa K.
**************************************************************
________________________________
De: David A Case <case.biomaps.rutgers.edu>
Para: Kepa K. Burusco <kekoburgo.yahoo.es>; AMBER Mailing List <amber.ambermd.org>
Enviado: Jueves 15 de noviembre de 2012 12:57
Asunto: Re: [AMBER] Energy Analysis from Trajectory
On Wed, Nov 14, 2012, Kepa K. Burusco wrote:
>
> Unfortunately, I am not yet an expert in the code so, my question is,
> would it be any problem to compute the total energy (and the single
> contributions: BOND, ANGLE, DIHED, VDW, EELEC, 1-4EL, 1-4NB) by using
> the imin=5 option rather than splitting the trajectory and running
> 1-step MD for every single snapshot?
This should be fine. There should also be no difference between minimization
and MD in terms of how the energies are calculated. If you find such a
difference, please try to make a simple test case that illustrates this.
Clearly, you could also take just a small number of frames from your
trajectory, and compare the imin=5 results to your 1step MD results.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 15 2012 - 08:30:02 PST
