On 2011-01-30 16.02, ms wrote:
On 29/01/11 05:08, Matt Chan wrote:
Perfect. This is great reading.
Thanks for the pointers Mark.
Matt
On 01/28/2011 06:50 PM, Mark Abraham wrote:
On 29/01/2011 9:57 AM, Matthew Chan wrote:
Hi,
I'm a first time GROMACS user. I've got 2 questions, which I'll ask
in separate emails. The first is about running EM on a charged
protein in vacuum.
I'm presently walking through some of the tutorials and trying to
simplify them for my purposes. One is the energy minimization of the
1AKI lysozyme protein. I would like to minimize this protein in
vacuum instead of solution as the tutorial demonstrates. Since the
genion program replaces water molecules with ions to balance the
charge of the system and there's no water, I'm having trouble running
the simulation with a neutral system.
My question is what effect does running a simulation with a charged
system have? I recall reading that something related to PME
calculations assumes the system is neutral, but it did not specify
whether it was referring to MD or EM. From the mailing list, I have
only been able to determine that running a charged system in solution
makes no sense biologically.
Some threads elsewhere cover these issues:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html
http://archive.ambermd.org/200712/0223.html
Mark
Since I have exactly the same needs (charged system in vacuum) I jump in...
In http://www.gromacs.org/Documentation/Errors
it says:
Note for PME users: It is possible to use a uniform neutralizing
background charge in PME to compensate for a system with a net
background charge. There is probably nothing wrong with this in
principle, because the uniform charge will not perturb the dynamics.
I'd like to comment that, this is tricky business. If your charges are
spread out homogeneously it may be OK, but in practice this is often not
the case (e.g. side chains on a protein). One should try to avoid this
if at all possible.
From the reading above, it seems that namd/amber implementations
already *implicitly* use this kind of compensation by ignoring terms in
the summation. Is it the same for GROMACS?
thanks,
M.
Gromacs does not ignore any terms in the simulations if I am not
mistaken. It also computes PME at every step in contrast to NAMD (don't
know about Amber).
--
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
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