[gmx-users] Dispersion correction for protein interfaces

[CHEN Pan]

Dear Jason,

According to my experience from one of our reviewers of our recent
submitted paper, the non-bonded parameters of aliphatic hydrocarbon of
GROMOS force fields didn't apply the LJ tail (dispersion correction) during
their development. You can also check the paper of Schuler et al. in 2001,
titled by "An improved GROMOS96 force field for aliphatic hydrocarbons in
the condensed phase", which used a twin-range cut-off strategy and did not
mention anything related to dispersion correction. Alternatively, it's the
best to communicate with the GROMOS group to validate. Hope this will be
useful for you.

Kind regards,
Pan


2014-03-28 17:55 GMT+01:00 Jason Grosch <jgrosch at umail.iu.edu>:

> Hello,
>
> I'm planning on studying several large protein clusters using the gromos
> 54A7 force field with the following cutoff parameters: rlist=1.0 nm,
> rcoulomb=1.0 nm (long range handled by PME), rvdw=1.4 nm, and the short
> range list will be updated every 10 steps.  I am interested in studying
> surface interactions, and I am uncertain if dispersion corrections is
> appropriate to use.  From the gromacs 4.5.6 manual and from previous posts,
> the dispersion correction is most appropriate for isotropic systems, and
> can be inappropriate for large interfaces such as lipid membranes.  The
> surface at proteins and protein clusters is anisotropic, does anybody know
> if the dispersion correction should be used with proteins with a 1.4 nm
> cutoff, as parameterized with gromos type force fields?  With such a
> relatively large vdw cutoff does the dispersion corrections even matter?  I
> don't see any differences when I use it, but I would like to be as correct
> as possible. Was the gromos force fields parameterized using dispersion
> corrections, I can't find a solid yes/no answer in the papers (I could have
> missed it)?  I haven't had much luck finding answers to these in previous
> posts, so any help or resources you can direct me to would be greatly
> appreciated.
>
> Thank You,
> Jason Grosch
>
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> Department of Chemistry, Indiana University, Bloomington.
> Email: jgrosch at indiana.edu
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-- 
Pan Chen
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