[gmx-users] Problem with replica exchange in vacuum

Xavier Periole X.Periole at rug.nl
Sun Nov 25 18:28:24 CET 2007

On Sun, 25 Nov 2007 19:00:47 +0200
> Hi all,
> I am performing a REMD simulation in vacuum. Although I minimized the energy 
>of each initial replica by using a stringent convergence criterion, after the 
>the third attempt, the system exploided because of a huge deviation in the 
>Lincs algorithm. 

What is the range of temperature you use? What time step you use?
At high temperature you need do decrease the integration time
step to avoid the increase of integration error due to the temperature.

Such a simulation, REMD in vacuo, is typically what you do not want
to do. You might think that you'll increase your sampling and thus
have better statistics. This won't give you any realistic picture of
your system.

At least put a continuum model! Even though ...


> Although I started to the simulation via low-energy structures, what may be 
>the probable reason for this? Is it because of vacuum?
> Thank you 
> Ozge
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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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