[gmx-users] some remarks about REMD and analysis

[David]

On Fri, 2005-10-28 at 19:43 +0200, Luca Mollica wrote:
> 
> Dear all, 
> 
> I would like to write down here some remarks about my Replica Exchange
> Molecular Dynamics simulation that finally thanks to all the advices
> has been successfully (partially performed). 
> 
> 1. The real problem of my simulation (described in the following post:
> http://www.gromacs.org/pipermail/gmx-users/2005-October/017715.html )
> was inded the temperature distribution and the difference of
> temperature I had between replicas. therefore, I have changed
> completely my mind and used this T setup: 
> 
> 280.0 281.0 282.1 283.2 284.3 285.6 286.8 288.2 289.6 291.0 292.5
> 294.1 295.7 297.3 299.1 300.8 302.7 304.6 306.5 308.5 310.6 312.7
> 314.8 317.1 319.3 321.7 324.1 326.5 329.0 331.6 334.2 336.8 339.6
> 342.3 345.2 348.1 351.0 354.0 357.1 360.2 363.3 366.6 369.8 373.2
> 376.6 380.0 
> 
> reducing the global time interval and also the difference of
> temperature between the single replicas according to Berk Hess
> advice. 
> Now the REMD is really ... exchanging replicas ! And everything sems
> to be fine and it works really well. Many thanx to all who gave me
> advices. 

But please check that you are getting exchanges at high temperatures as
well. And are you using NPT? Without NPT you simulate the high
temperatures at high pressure, and hence the high temperatures are
almost useless for analysis. However, with NPT you need a more evenly
spread T interval.

> 
> 2. A question/ suggestion: REMD implementation is only set up for
> single CPU .... but what about giving the possibility of distributing
> a replica on many CPUs instead of using one processor only ? Is it a
> choice or are there any problems of implementationof such a
> feature ?? 
> 
> Bye 
> 
> LM 
> 
> 
>   
> -----------------------------------------------------------------------------
> 
> Luca Mollica
> ZRL-IBM Research Center
> Saumerstrasse 4
> 8803, Rueschlikon (Zurich)
> CH
> 
> Tel: 0041 - 447248217
> 
> email:        YLU at zurich.ibm.com  
> email(alt): ZRLYLU at ch.ibm.com  
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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