[gmx-users] restart an amber run in gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Wed Nov 21 22:08:17 CET 2007

servaas michielssens wrote:
> I used amb2gmx.pl (from http://chemistry.csulb.edu/ffamber/) to convert
> an amber topology and restart file to a gromacs topology and structure
> file and tried to continue the simulation in gromacs. I got the
> following error message:
> Constraint error in algorithm Lincs at step 0
> t = 0.000 ps: Water molecule starting at atom 4642 can not be settled.
> Check for bad contacts and/or reduce the time-step. Wrote pdb files with
> previous and current coordinates
> It seems strange to me that this error occurs as there was no problem
> with this simulation in amber. (it ran a few ns in amber).
> I tried to run it after minimalization and this worked fine. So there
> seems to be a problem while converting the files, I am new to gromacs
> and I don't really have a clue how to find the cause of this problem,
> perhaps some of you also tried to continue a amber run in gromacs?

Judging by my interpretation of your last email, you probably did a more 
radical change of ensemble than you think you did. Both AMBER and 
GROMACS are approximating some true ensemble, and there's no reason to 
assume that a configuration from one will be equilibrated in the other.


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