[gmx-users] REMD general protocol ...

[massimo sandal]

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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