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

[X.Periole]

> 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
> 

The spaces look large to me for this size of system ! The
best would be to plot the Epot distribution and look at 
the
overlap of the curves. That is what determines the 
exchange
ratio.
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 ?

Best
XAvier

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XAvier Periole
MD - Group
University of Groningen
The Netherlands
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