Justin M. Shorb wrote:
Greetings:
I have been having trouble running any energy minimization with any sort
of system. I have small polypeptides in water, and then large proteins
in water with the same error message:
No matter what run parameters I get, I always get ci = -2147483648. Even
different systems. (This, I realize is simply numerically infinity). If
I try running with ns_type = simple, the em runs until it hits around 35
and then says it didn't converge. Since I am running grompp_d -v, I get
that there are certain atoms that have infinite potential. But,
depending on the system, the atom type (solvent or molecule) changes.
This suggests a problem with your force field and/or topology.
I have noted that previous posts have been answered with an admonition:
"Find out which atoms are infinite force, and then fix it." I suppose I
could go through, find the atoms and remove those waters that overlap,
but shouldn't this be taken into account by the genbox_d program? I also
have tried to increase the vdw radii in the vdwradii.dat file to have it
delete more waters. But, even after having 60 fewer waters around a 88
kD protein, the system still fails to energy minimize.
This suggests that the source of the problem isn't that these atoms
start life too close together, but maybe they're moving too close
together because of some other problem? (Unless the error is always
happening before the first EM step)
Given that this seems to be a common problem in solvating a system, are
there better options (options for genbox??) than running the following
shell commands? The em.mdp file is also shown below.
That all seems fine.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
