[gmx-users] Re: NVE problems

[istvan at kolossvary.hu]

Thanks for the hints and the reference. I am using SPC water and I suppose I 
use settle, because the error message says that some water could not be 
settled. However, I don't know how to "settle" explicitly. I may have 
overlooked it, but I don't seem to find anything about settle in the manual. 

Thank you very much, 

  Istvan 


David van der Spoel wrote: 

> On Sat, 27 Dec 2003 istvan at kolossvary.hu wrote: 
> 
>>Hi,  
>>
>>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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> 
> -- 
> David.
> ________________________________________________________________________
> 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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> 
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