Felipe Villanelo wrote:
Hi everybody
I want to run a EM, but grompp give me this Note:
The sum of the two largest charge group radii (0.305345) is larger than
rlist (1.000000) - rvdw (0.900000)
I have read in the gmx forums, that this is a problem from the
designation of charge groups, but I have make the topology with Gromacs
pdb2gmx and there is no other molecule, different of protein with
standard residues.
Even if I try to run the EM just with the protein in vacuum, the error
is the same.
So the problem cames from pdb2gmx which is not making the correct charge
groups assignation from a simple protein.
But when I use the AMBER ff, this problem dissapear. However, I need to
use the GROMOS96 ff (In the future, I want to simulate the protein with
a ligand parametrizied with this ff)
I could try to change the rlist/rcoulomb and rvdw, but I think that this
is not a real solution.
The problem does not come from pdb2gmx; it comes from your .mdp file. The
settings specified are incorrect for Gromos96 force fields. For Amber, you
receive no error because all charge groups consist of only one atom,
essentially, there are no groups.
For Gromos96 force fields, rlist=rcoulomb=0.9 and rvdw=1.4 are correct settings.
I suspect you're trying to use some sort of switch or shift function, and
hence rlist > rvdw. You shouldn't. vdwtype=cutoff and coulombtype=PME are the
best settings.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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