Dear David:
Thanks a lot for your reply. You are absolutely right! All the charges
in the tpr file is zero now.
This does not make much sense to me though, as the group I selected
with "tpbconv" does not include all the atoms. I also tried to use
other groups such as POPC or Protein and none of them give me sensible
results (the charges are not all set to zero). Is this supposed to be
a bug?
Thanks,
Bin
On 2010-12-03 08.45, BIN ZHANG wrote:
Hi, all:
I was trying to use "tpbconv" to modify the tpr file with the
command:
tpbconv -s %s.tpr -nsteps -1 -zeroq -n index -o final.tpr
It basically sets the charge of one group to zero. However, when I
perform mdrun -rerun, all the coulombic energies are zeros, i.e.,
Coulomb-(SR), Coul.-recip. This really does not make sense since I
still
have atoms in other groups that are charged. I was using
gromacs4.0.7.
Please check using gmxdump that there still are charged groups left
in your tpr file.
Has anyone seen this before? What exactly is the correct way to
zeroize
the charge for a group of atoms?
Thanks,
Bin
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
From: Olga Ivchenko <olga.ivche...@gmail.com>
Date: December 3, 2010 12:31:50 AM PST
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] proton proton transfer
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Hi Erik,
I think also I can try proton-proton transfer with gromacs later
when it will be implemented.
best,
Olga
2010/12/2 Erik Marklund <er...@xray.bmc.uu.se>
Olga Ivchenko skrev 2010-12-02 13.30:
Dear gromacs users,
I want to simulate proton transfer between water and another small
molecule in gromacs. In the end I should have the velosity of proton
proton exchange. Please can you advice me which method is better to
use for this in gromacs.
I read about umbrella sampling, but may be there is other techniques?
Yours sincerely,
Olga
I am working on a protocol to include proton transfer in classical
gromacs simulations. Unfortunately it will note be ready for at
least a month, so if you're in a hurry you'll have to do it with
e.g. QM/MM.
Erik
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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