From: "Berk Hess" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: [email protected]
Subject: [gmx-users] FW: rvdw
Date: Fri, 20 Jul 2007 09:11:35 +0200
From: "Yin Jian" <[EMAIL PROTECTED]>
To: "Berk Hess" <[EMAIL PROTECTED]>
Subject: rvdw
Date: Thu, 19 Jul 2007 12:53:00 +0800
Hi Dr Berk Hess,
I am now using gromacs in simulation of coarse-grained model. As a
multi-scale
Coarse-graining, the LJ cutoff in gromacs is not fit this case. Since
our model
have particle with one order difference in their vdw radii. So the idea
of fix is to
change the original scheme at the source level. For example use a scalar
variable
to get the cutoff radius for each particle by multiplying the scalar to
their own
vdw radius. That would solve our problem easily. This dynamic LJ cutoff
would
be a second option relative to the current static (sinle-valued) cutoff.
Do you think gromacs development group would like to make a change like
that so that we may get our job done without too much bothering.
Thanks in advance.
Yin Jian (PhD)
Research Staff,
Singapore-MIT Alliance (SMA)
National University of Singapore
Singapore
What do you mean with "does not fit the case"?
You do not explain what you want exactly,
but I think the current Gromacs setup would work.
Or do you think you could gain performance with your proposed scheme?
That would only be the case if you have regions with only small and only
big particles.
If the small and big particles are mixed, you would not gain much.
In general it is a bad idea to have a coarse grained model
with particles sizes that differ by an order of magnitude.
Berk.
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