[gmx-users] minimization

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 13 12:56:22 CEST 2009

Morteza Khabiri wrote:
> Dear Tsjerk
> Thanks for your suggestion...actually It is a crystal structure...the
> problem happen when I want to minimize the structure in vacuum....the box
> size is enough...but the problem is that the minimization is fine with
> gromacs forcefield but it is not ok with OPLSAA forcefiled....

That seems intrinsically improbable, unless the oplsaa .hdb and .tdb 
files are not coping with the structure (somehow) and generating a 
broken starting configuration and/or topology. What was the final PE and 
maximum force from the gromacs forcefield EM? I suggest you look 
carefully at the post-pdb2gmx oplsaa structure for steric clashes, 
unsatisified valences, etc., and then look at the progress of the 
corresponding minimization. You should see evidence of whatever is wrong.


> I tried to
> minimized structure well  by gromacs force file and the I took the
> minimized structure from gromacs forcefield and then I tried it in OPLSAA
> and the problem was the same as before... I also cut my structure to some
> pieces ( which I think that it is not reasonable) but I did it but still
> it is not working....and the interesting point is that the protein is
> working by gromacs forcefield well without any problem but when I want to
> use the OPLSAA force field the problem
> start and I could not minimized my system..I also try the AMBER forcefield
> but the AMBER also didi not work and the result was the same as OPLSAA,
> system was exploding.......when I want use all atom the problem appear and
> I really don't know how to manage it..I already tried different coulomb
> type algorythm and also different integrator,, different time
> step..different emtol........but none of them working.......
> I would be happy if somebody could suggest me how could I manage it with
> all atom forcefield...
> thanks
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