[gmx-users] lincs contraint failure

David van der Spoel spoel at xray.bmc.uu.se
Tue Feb 28 08:53:52 CET 2006

Mark Abraham wrote:
> Nuri A Temiz wrote:
>> Dear Mark
>> The mdp file is how it should be. I also did a cut-off run from the 
>> same starting point and it runs. For the PME i have tried to decrase 
>> the time step to 1 fs. that did not work
>> either. The protein is exploding and simulations is crashing. 
> OK. Take your cutoff and PME .tpr files and compare them. The simplest 
> thing to do is to "gmxdump -s cutoff.tpr > cutoff.txt" and similarly for 
> PME. Then use diff to compare them. This will make absolutely clear 
> whether you are doing the same thing with different electrostatic 
> treatment or not. Also visualize the exploding and non-exploding runs to 
> see if that enlightens you.
You can do this in one go using:

gmxcheck -s1 cutoff -s2 pme | less

> Mark
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David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se

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