Ondrej Marsalek wrote:
On Wed, Nov 4, 2009 at 20:41, Justin A. Lemkul <jalem...@vt.edu> wrote:
Ondrej Marsalek wrote:
I thought that this was needed to convert the hydrogens to virtual
sites, based on reading section 6.5 of the manual and some other
things. Is this not correct?
I don't believe constraining angles is necessary. The manual only refers to
fixed bond lengths. If you're looking for an example to follow, I would
suggest running the lysozyme benchmark described in the GROMACS 4 paper;
OK, so now I am mildly confused. I have downloaded the benchmarks pack
(gmxbench-3.0.tar.gz) from the GMX website. The pme.mdp file for
lysozyme indeed says "constraints = all-bonds". On the other hand, the
topology contains virtual sites in the list of atoms, but there are no
[virtual_site?] sections. And the timestep is 4 fs. Could someone
please help me clarify this?
That's the old benchmark set (version 3.0), and has nothing to do with version
4.0, for which I do not believe there is an actual set of benchmarks. I was
merely referring to the described procedure, parameters, and results obtained in
the GROMACS 4 paper.
-Justin
Thanks,
Ondrej
the
parameters used are nicely detailed. I got reasonable results using
"constraints = all-bonds," but if that is not correct, perhaps someone else
can comment.
-Justin
Ondrej
On Wed, Nov 4, 2009 at 20:07, Justin A. Lemkul <jalem...@vt.edu> wrote:
Ondrej Marsalek wrote:
Dear GROMACS users,
I would like to substitute hydrogens in a protein with virtual sites
to allow for the 4-5 fs timestep mentioned in the GROMACS 4 paper and
several other places. So far, I have not found an example or a
tutorial that would involve this, so I want to create a
straightforward example. I have taken the 2KO3 structure from the PDB
and went through this sequence of commands:
pdb2gmx -v -f 2KO3.pdb -o initial-vacuum.gro -ff oplsaa -water tip4p
-vsite hydrogens -ignh
editconf -f initial-vacuum.gro -o initial-box.gro -c -d 1 -bt cubic
genbox -cp initial-box.gro -cs tip4p.gro -p topol.top -o conf.gro
grompp
I also provided a pretty standard grompp.mdp, that contains
"constraints = h-angles". I get the following error:
-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: vsite_parm.c, line: 779
Fatal error:
Automatic parameter generation not supported for Virtual site 3 atom 4
for this bonding configuration
-------------------------------------------------------
I am not sure what the problem is. I would appreciate and help on the
use of this feature, pointers to resources, or a working example.
Reading the manual and searching did not help as much as I would like.
Have you tried specifying either "all-bonds" or "h-bonds" for
constraints?
I think "all-bonds" is the most commonly-used option. Any specific
reason
for using "h-angles"?
-Justin
Thanks,
Ondrej
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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