simon sham wrote:
Hi,
I have two questions about using the charmm force field.
1. Do we still need to use the two perl scripts, convert_charmm_
to_gromacs.pl and fix_top_for_charmm.pl?
No.
2. I got the following note when I tried to do energy minim. with grompp:
NOTE 1 [file topol.top]:
The largest charge group contains 12 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
Is this a problem?
Yes. CHARMM topologies should not use charge groups. You should invoke pdb2gmx
with the -nochargegrp option to create a proper topology.
-Justin
Thanks for your insight!
Simon
--
========================================
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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