[gmx-users] Re: Simulation of 2D lattice model

Bogdan Costescu bcostescu at gmail.com
Thu Jan 17 12:03:46 CET 2013

On Thu, Jan 17, 2013 at 10:59 AM, James Starlight
<jmsstarlight at gmail.com> wrote:
> thank you for so detailed explanation.

You're welcome. Now it's up to you to use it :)

> Now it's only intresting to me
> if it possible to change vdw radius (assuming it as the distance from
> center of atom to it outer electronic shell)?

Yes, it's possible.

> E.g I want to change
> such value for each node in my lattice model (e.g for CH2 united atom
> that value might be > 1.5 and I want dicrease it to the 1 A ( as for
> simple carbon). Might I do it via some simplest modifications in the
> nonbonded.itp or should I do that by means of changes in
> sigma/epsillon terms (Which I also must express from A(c6) and B(c12)
> based on gromac's combination rules) ?

If nonbonded.itp for your chosen force field is expressed in
sigma/epsilon (I guess that this is the case because you talk about an
existing value for sigma), then it's only a matter of changing the
sigma parameter of that atomic species.

Keep in mind that this is only a description of the change - it
doesn't guarantee that the change is valid. If I'd be a reviewer I'd
ask for a reason for changing one of the parameters (sigma) and
keeping the other (epsilon) constant.


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