[gmx-users] charge group radii larger that rlist-rvdw

[Justin A. Lemkul]

Kavyashree M wrote:
> Sir,
> 
>      System is a protein with 123 aa. No modifications were made on the 
> pdb file,
> and it was submitted to pdb2gmx by removing all HETATMs, retaining only 
> protein
> atoms. topology was created entirely by pdb2gmx and no other molecule 
> was introduced.
> 
>      I will go through the OPLSAA paper, but if I increase rlist to 
> 1.4nm without reducing
> rvdw according to "The Origin of Layer Structure Artifacts in 
> Simulations of Liquid Water"
> - JCTC, 2006, 2, 1-11, will it not cause orderedwater shell during 
> simultion?
> 

You're using PME.  In the first paragraph of the introduction, it is stated that 
the spurious effect does not occur with PME.

-Justin

> 
> Thanking you
> M. Kavyashree
> 
> On Sat, Jan 22, 2011 at 12:27 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Kavyashree M wrote:
> 
>         Sir,
> 
>           What exactly can be wrong with the topology? As I tried with
> 
> 
>     I don't know, what's in your system?  Was the topology created
>     entirely by pdb2gmx, or have you introduced some other molecules
>     that you've parameterized?
> 
> 
>         different PDBs of same structure at higher resolutions too, I am
>         getting
>         almost similar charge group radii, so can you kindly elaborate about
>         what can go wrong in the topology to get such values?
> 
> 
>     Large charge groups indicate that a fair number of atoms have been
>     included in the same charge group.  Usually only two or three atoms
>     are in a charge group, rendering them fairly small.  With PME, the
>     effects may not be that large, i.e.
>     http://lists.gromacs.org/pipermail/gmx-users/2010-November/056219.html,
>     but it's still worth investigating what your largest charge group is
>     that's causing this problem.  If the topology is sound and is based
>     entirely upon standard force field files, it may suffice to simply
>     increase rlist to 1.4 nm, leaving all the other cutoffs at 1.0,
>     which I believe is standard for OPLS (but don't just take my word
>     for it).
> 
>     -Justin
> 
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     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
> 
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-- 
========================================

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

========================================