[gmx-users] LINCS deviation

Alan Dodd anoddlad at yahoo.com
Mon Apr 24 20:54:32 CEST 2006

Presumably this is with a standard, non-modified
forcefield.  One thing that might be worth trying (as,
perhaps, a last resort) is reducing the timestep. 
It's a bad thing to have to do, because it reduces
speed massively, but might help equilibrate your
system and reduce whatever bad contacts are causing
the problem.  You could then crank up the timestep
again to something more productive.
Running at a lower temperature for a while, again,
might allow the system to settle down.

--- Ashutosh Jogalekar <ajogale at emory.edu> wrote:

> Hello
> I am simulating a regular seven residue peptide:
> HHQALVFFA, in the  
> form of a beta sheet with five strands.
> The EM went ok. The structure looks ok. But I am
> still getting the  
> error about the LINCS constraint deviation during
> the posit. restr. MD.
> Could someone suggest what I could do to get rid of
> the problem?
> dt= 0.002
> nsteps= 10000
> constraints= all-bonds
> tau_p= 1.0
> Thanks
> Ashutosh Jogalekar
> Emory University
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