[gmx-users] Problems with the SHAKE-algorithm

[David van der Spoel]

Björn Fischer wrote:
> Dear gromacs users,
> 
> I am trying to run a nonane gas phase system (custom force field). It the
> beginning, everything looks ok, but after some time an error like this
> occurs:
> 
>  > >Constraint error in algorithm Shake at step 74147
>  > >Wrote pdb files with previous and current coordinates
>  > >Inner product between old and new vector <= 0.0!
>  > >constraint #1 atoms 191 and 192
>  > >   i     mi      j     mj      before       after   should be
>  > > 190  14.06    191  15.03     4.25365     1.60942     0.15400
>  > > 191  15.03    192  15.03     4.19749     1.90346     0.15400
>  > > 192  15.03    193  15.03     0.08362     0.88827     0.15400
>  > > 193  15.03    194  15.03     0.40714     0.46199     0.15400
>  > > 194  15.03    195  15.03     4.28246     5.11853     0.15400
>  > > 195  15.03    196  15.03     3.89289     4.69530     0.15400
>  > > 196  15.03    197  15.03     0.30450     0.33541     0.15400
>  > > 197  15.03    198  14.06     0.28803     0.34247     0.15400
> 
> The timestep, at which this happens, varies with the (randomly
> generated) start configuration. The temperature of the system rises
> about one order of magnitude, and shortly afterwards all the output
> in the md.log file is NaN.
At high temperature you need a shorter time step. Are you sure you don't 
want to use T-coupling?

> 
> Do you have any suggestions where to look for the source of the problem ?
> 
> Thanks in advance for your help!
> 
> Björn
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-- 
David.
________________________________________________________________________
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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