On 2011-01-30 17.08, ms wrote:
On 30/01/11 15:41, David van der Spoel wrote:
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.
Oh, this is very bad news. Could you elaborate on that? (I have a CG
model where this would be badly needed).
With homogeneous I mean a solution of ions.
Can spreading neutralizing charges along the other chain atoms be a
viable alternative for enough atoms and enough low charge? (e.g. if I
have 100 atoms and a +5 net charge, adding a -0.05 charge on all others?)
Sounds like a recipe for disaster. Try looking for solutions with
explicit counter ions.
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).
Thanks.
m.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
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