[gmx-users] REMD general protocol ...

[rama david]

Thank you Massimo sandal, Justin and mark ,

I also goes through the article and GMX archive.
But I confuse with the protocol ( I am naive in REMD .
So I want to conform protocol from the Expert and experience person )

I will be grateful to you  for your suggestion.





On Tue, Apr 2, 2013 at 6:45 PM, massimo sandal <devicerandom at gmail.com>wrote:

> I would look on some paper which temperature ranges and conditions
> (NPT/NVT) were used for systems of a similar size and with a similar aim.
>
>
> 2013/4/2 rama david <ramadavidgroup at gmail.com>
>
> > Dear friends ,
> > Thank you justin and Mark for your suggestion
> >
> > I increases my temp range from 310-360 K
> > Now I get 20 replicas .
> >
> > Is in such large temp range wlll it be good to use NPT.
> >
> > Would you tell me the temp differences in which box instability generally
> > arises ..
> >
> >
> >
> > Is my working-flow right or need to change much
> >
> >
> > Thank you
> > With Best Regards..
> >
> >
> >
> >
> > On Tue, Apr 2, 2013 at 5:08 PM, Erik Marklund <erikm at xray.bmc.uu.se>
> > wrote:
> >
> > >
> > > On 2 Apr 2013, at 13:30, Justin Lemkul <jalemkul at vt.edu> wrote:
> > >
> > > >
> > > >
> > > > On 4/2/13 7:13 AM, rama david wrote:
> > > >> Dear friends,
> > > >>           I am naive to the Replica exchange Molecular dynamics (
> > REMD).
> > > >> I have plan to use REMD for temp. 310-320 K to my system.
> > > >> I  thoroughly search the Mailing-list Archive for the REMD problem.
> > > >> It was a really helpful to start.
> > > >>
> > > >>  My system consist of peptide + water.
> > > >>
> > > >> I used the following work-flow, Would you please help me to find out
> > > >> my mistakes...
> > > >>
> > > >> 1. energy minimesation for peptide  + solvent
> > > >> 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file )
> > > >> 3. Make tpr file for each nvt run
> > > >> 4. Then separate  equilibration for each temp ( 4 equilibration
> steps
> >  )
> > > >> 5. Then made NPT.mdp file for each temp ( 4 temp )
> > > >> 6. Then again equilibration for NPT at 4 temp.( 4 equilibration
> >  steps )
> > > >> 7.   Then run md production  with -replex 1000  -multi 4  command ..
> > > >>
> > > >> To determine the temp I used web-server
> > http://folding.bmc.uu.se/remd/
> > > >>
> > > >> Please suggest me any improvements that are  possible to implement
> in
> > > >> my work flow.
> > > >>
> > > >
> > > > Such a narrow range of temperatures defeats the purpose of using
> REMD.
> > > Normally, a much larger range is used over many more simulations.  For
> > > near-ambient temperatures, NPT can be used, but if you include much
> > higher
> > > temperatures, you should use NVT due to box instability upon exchanges.
> > > >
> > > > -Justin
> > >
> > > Sure, the enhanced sampling is basically gone, but you can deduce
> > > temperature dependences from such simulations and to some extent
> benefit
> > > from the mixing, can't you?
> > >
> > > Erik
> > >
> > > >
> > > > --
> > > > ========================================
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Research Scientist
> > > > 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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