[gmx-users] Re: REMD ... again a problem with analysis (on the fly)

[David van der Spoel]

On Tue, 2005-10-25 at 10:50 +0200, Luca Mollica wrote:
> 
> Hi, 
> 
> the temperature distribution for my system is the following: 
> 
> 250.0 254.0 258.3 263.0 267.9 273.2 278.8 284.7 291.0 297.5 304.4
> 311.6 319.1 327.0 335.1 343.6 352.4 361.5 371.0 380.7 390.8 401.2
> 411.9 423.0 434.3 446.0 
> 
> But I would like to point out a thing about my simulation that could
> help to find a solution to my problems: my system contains 17.000
> (more or less) water molecule: could this fact influence in any way
> the proper work of REMD ?? I am trying to set up a simulation with a
> denser replica space and a less temperature difference: also the
> closest replica have a difference of about 20 kJmol-1 ..... 
You need to take linear spacing between the replicas, because at higher
T the density becomes lower and hence the energy becomes higher. A
linear spacing compensates for this. You may also need to use more
replicas.
> 
> L 
> 
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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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