[gmx-users] Re: REMD ... again a problem with analysis (on the fly)
X.Periole at rug.nl
Tue Oct 25 11:10:38 CEST 2005
> the temperature distribution for my system is the
> 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
The spaces look large to me for this size of system ! The
best would be to plot the Epot distribution and look at
overlap of the curves. That is what determines the
Did you observe any exchange ? What is your exchange ratio
Short simulations are able to give a good approximation of
the exchange ratio, no need of equilibration of the system
for this. It only depends on the overlap of consecutives
Epot or Temp distributions.
> 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 ??
Not really ! I don't see why it would.
> 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 .....
That number is extracted from your the log files ? or is
it the difference between average Epot ?
MD - Group
University of Groningen
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