[gmx-users] Pre-equilibrated CHARMM lipid bilayers
Peter C. Lai
pcl at uab.edu
Thu Dec 20 12:33:09 CET 2012
You can always see if you have any by looking at cgnr column of the protein
.itp file. If each atom is in its own chargegroup (the cgnr increments by
atom) then it's fine.
Is this charmm36 (when did you install this from the website?)or
27 (what gromacs version)? There were two chargegroup problems fixed in two
successive versions. First, I think 4.5.4 Charmm27 removed all chargegroups
for by default in the .rtp files. Then, the charmm36 upload was fixed to
do that too. However, I am not sure what versions has fixed terminii.
In gromacs 4.5.3 and the charmm36 from that time period would generate
capping groups with a single large chargegroup.
Anyway, Grompp will give you an idea if you have a really large chargegroup
when it gives you the notice about them; if your largest chargegroup is
comparable to the van der waals diamater of two atoms I don't think there is
anything to worry about. If you do have a lot of large chargegroups,
apparently you might run into cutoff artifacts but I'm not sure exactly.
On 2012-12-20 01:37:25PM +0300, James Starlight wrote:
> what errors might occurs if I've missed -nochargegrp option while
> parametrising my protein by means of pdb2gmx?
> 2012/12/20 Peter C. Lai <pcl at uab.edu>:
> > (As a side note, Gromacs shouldn't use charge groups when using
> > all-atom charmm forcefields.)
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