[gmx-users] CHARMM forcefield

[Justin A. Lemkul]

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
> 

-- 
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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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