[gmx-users] NVE problems

David van der Spoel spoel at xray.bmc.uu.se
Sat Dec 27 21:11:01 CET 2003

On Sat, 27 Dec 2003 istvan at kolossvary.hu wrote:

>I posted a message right before Christmas (gmx-users digest, Vol 1 #1166) 
>about problems with NVE. I have a feeling that the nsgrid error that I 
>mentioned is not specific to the problem, it just shows a general numerical 
>instability due to the NVE simulation. In other cases Gromacs blows up with 
>other numerical errors. In any case, I guess the simplest way to present the 
>problem is to ask why should Gromacs blow up on alanine dipeptide in a 3x3x3 
>nm box using NVE instead of NPT? I can hardly think of anything simpler. The 
>system was minimized, PR-equilibrated (FF was OPLS-AA), but then a fully 
>unconstrained run with PME that would normally run without problems in NPT, 
>blows up after only 1 ns using a 1 fs time step when I turn off temperature 
>and pressure control. Shouldn't a 1 fs time step be adequate for NVE without 
>LINCS/SHAKE? Can anyone experienced with NVE in Gromacs help me? 

I think it is too long a time step. 0.5 fs is probably the maximum for 
stability with T coupling, but you may even need shorter without. Check 
for energy components. Are bond/angle energies getting out of hand? What 
water do you use? Is it with settle?

>Many thanks, 
>  Istvan Kolossvary 
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>gmx-users at gromacs.org
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David van der Spoel, PhD, Assist. 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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