[gmx-users] FW: rvdw

Yin Jian smayinj at nus.edu.sg
Fri Jul 20 09:40:33 CEST 2007

Thanks, Hess.
The idea behind this order difference in coarse-grained scaling size
is to keep solvent relative smaller to the target particle, or say
after coarse-graining, solvent is still solvent and solute is still


-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Berk Hess
Sent: Friday, July 20, 2007 3:17 PM
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] FW: rvdw

>From: "Berk Hess" <gmx3 at hotmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] FW: rvdw
>Date: Fri, 20 Jul 2007 09:11:35 +0200
>>From: "Yin Jian" <smayinj at nus.edu.sg>
>>To: "Berk Hess" <gmx3 at hotmail.com>
>>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
>>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
>>of fix is to
>>change the original scheme at the source level. For example use a
>>to get the cutoff radius for each particle by multiplying the scalar
>>their own
>>vdw radius. That would solve our problem easily. This dynamic LJ
>>be a second option relative to the current static (sinle-valued)
>>Do you think gromacs development group would like to make a change
>>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

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.


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