Hi Berk and others,
I have been wondering if there was another way to treat the large charge
groups for the CHARMM forcefield(s) in GROMACS, rather than using the
-nochargegrp option.
The reason I ask is because changing every atom to be in individual
charge groups changes the forcefield (albeit slightly) from its original
implementation and it would be good to be able to use the forcefields in
as close a way as possible as to how they were originally used in CHARMM.
I suppose another way to do it is to increase the cutoff's, however
changing the cutoff's from their original intended values is also
undesirable and this can also significantly impact on performance.
Whether this is better or worse (in the sense of the difference to how
the forcefields were originally used in CHARMM) than using -nochargegrp
I am not sure. I also noticed that in version 4.5 there is a rlistlong
parameter, could this be used to account for the large charge groups
rather than increasing other cutoff's?
Can anyone think of any other ways to do this? I have no idea if it be
easy/possible to implement an option to use the CHARMM approach for
treating charge groups (as I understand it when any atom is within the
cutoff then the whole charge group is included).
Sorry for the fairly long message and thanks for any insights you can give.
Tom
Berk Hess wrote:
Hi,
No, you should never change the charges in a force field!
Run pdb2gmx again with the -nochargegrp option.
That will make the size of all charge groups a single atom.
This will be done automatically in the 4.5.2 release which will be out soon.
Berk
------------------------------------------------------------------------
Date: Fri, 17 Sep 2010 02:32:31 -0700
From: meetnah...@yahoo.com
To: gmx-users@gromacs.org
Subject: [gmx-users] ARG Charmm gmx 4.5.1
Dear Gromacs Users,
I am using plain cutoff for my 12-mer protein.
The grompp reports ARG to have a big charge group. this was also
highlighted in the following mail
http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html
I was just think if changing the charges on these atoms would help,
from
13 CT2 1 ARG CD 4 0.2 12.011 ; qtot 1.2
14 HA 1 ARG HD1 4 0.09 1.008 ; qtot 1.29
15 HA 1 ARG HD2 4 0.09 1.008 ; qtot 1.38
16 NC2 1 ARG NE 4 -0.7 14.007 ; qtot 0.68
17 HC 1 ARG HE 4 0.44 1.008 ; qtot 1.12
18 C 1 ARG CZ 4 0.64 12.011 ; qtot 1.76
19 NC2 1 ARG NH1 4 -0.8 14.007 ; qtot 0.96
20 HC 1 ARG HH11 4 0.46 1.008 ; qtot 1.42
21 HC 1 ARG HH12 4 0.46 1.008 ; qtot 1.88
22 NC2 1 ARG NH2 4 -0.8 14.007 ; qtot 1.08
23 HC 1 ARG HH21 4 0.46 1.008 ; qtot 1.54
24 HC 1 ARG HH22 4 0.46 1.008 ; qtot 2
to
CD 0.18
HD1 0.06
HD2 0.06
NE -0.7
HE 0.4
CZ 0.6
NH1 -0.8
HH11 0.5
HH12 0.5
NH2 -0.8
HH21 0.5
HH22 0.5
The above transformation of charges seems reasonable.
Would like to know if this is okay...
Best,
nahren
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