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.
Mark
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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