[gmx-users] LINCS WARNING: How to correct LINCS WARNINGs
spoel at xray.bmc.uu.se
Sat May 3 15:50:01 CEST 2003
On Sun, 2003-05-04 at 04:10, Mr.Sridhar wrote:
> Dear gmx users,
> I was running a MD simulation of a 49 aa protein in spc216 water. I used
> the GROMOS96 force field. The .mdp file is attached. The program ran well
> for some and then started giving LINCS warnings like "relative constraint
> deviation after LINCS:" and " bonds that rotated more than 30 degrees:"
> etc. The program got terminated prematurely after some such warnings.
> Could anybody explain what these warnings mean and how to overcome them.
> Thanking you
there's two small things in your mdp file: you do not explicitly select
PME for Coulomb type, and hence you are simulating with a cut-off, only
rvdw > rcoulomb, that means you have a twin range cut-off. While this
shouldn't give any problems in principle, it may not be what you want.
Second thing is that tau_p is a bit short, I recommend at least 1 ps.
This may actually lead to instabilities like you showed.
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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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