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

[Justin A. Lemkul]

Kavyashree M wrote:
> Sir,
> 
>      Yes sir I am using PME. And one more thing I noticed was, the 
> protein has
> 7 disulphide bonds, so when I reduce all the cystine to cysteine or to 
> alanine,
> the the sum of charge group radii reduces from 0.31..nm to 0.30..nm and 
> also the
> value of this is identical in case of alanine mutation or cysteine mutation.
>     I finalised on the value of rlist = rcolomb = 1.35nm so as not to 
> take risk.
> is that fine?
>    

As I said before, read the OPLS paper.  1.35 nm does not sound right.

-Justin

> Thank you
> M. Kavyashree
> 
> On Sat, Jan 22, 2011 at 6:26 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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>
>         <mailto: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> <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 <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

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