[gmx-users] Re: Long-range (LR) energies in gromacs v3.3.3

[Justin A. Lemkul]

Shankar Prasad Kanaujia wrote:
> Dear justin,
> sorry for writing person mail.
> I am attaching the .mdp file.
> 

You are using a shift potential for vdwtype (and you haven't applied it 
correctly - read the manual.)  Therefore, LJ terms are cut off at rvdw (the LJ 
term is zero beyond this point) and you are not seeing a long-range LJ term. 
Using PME for coulombtype means that the "long range" component of the 
electrostatic nonbonded energy is in Coul.-recip.

-Justin

> thanking you.
> -- 
> Yours Sincerely,
> Shankar Prasad Kanaujia
> Research Student
> C/O - Dr. K. Sekar
> Bioinformatics Centre, SERC
> Indian Institute of Science, Bangalore-12
> Phone - 9480258032
> Office - 080-2293-3059
> 
> 
> 
> On Sat, May 30, 2009 at 9:00 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
>     Please keep all correspondence on the gmx-users list.  I do not
>     advertise myself as a private tutor :)
> 
> 
>     Shankar Prasad Kanaujia wrote:
> 
>         Dear Justin,
>         I have done simulation of protein-ligand complex using gromacs
>         v3.3.3.
>         The g_energy gives LJ-14, Coulomb-14, LJ-SR, Coulomb-SR energies,
>         however, it does not give LJ-LR and Coulomb-LR energy.
> 
>         what could be the reason ?
> 
> 
>     It would be useful if you posted your .mdp file.  Without it, I can
>     only guess why the LJ-LR term is missing.  There is no such term
>     Coulomb-LR.
> 
>     -Justin
> 
> 
> 
>         thanking you.
>         -- 
>         Yours Sincerely,
>         Shankar Prasad Kanaujia
>         Research Student
>         C/O - Dr. K. Sekar
>         Bioinformatics Centre, SERC
>         Indian Institute of Science, Bangalore-12
>         Phone - 9480258032
>         Office - 080-2293-3059
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
> 
> 
> 
> 
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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