[gmx-users] REMD general protocol ...

[rama david]

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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