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

James Starlight jmsstarlight at gmail.com
Thu Jan 17 13:51:53 CET 2013


thanks againfor explanation.

So  if I have force field with the C6/C12 terms (instead of
sigma\epsilon) I need to express sigma (which correspond to the Rmin
in LJ equation) as the (C12/C6)^0.5. Than if I want to increase sigma
( and consequently to increase vdw radius of my atom) I  must to
increase c12 or decreace C6 terms.  Does it correct in general ?

2013/1/17 Bogdan Costescu <bcostescu at gmail.com>:
> 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.
> Cheers,
> Bogdan
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