[gmx-users] Cut-offs using CHARMM27 ff

[Roland Schulz]

On Wed, Dec 1, 2010 at 4:30 PM, Hassan Shallal <hshallal at pacific.edu> wrote:

>  Dear Gromacs users,
>
> I am trying to use CHARMM27 taking the simulation conditions of two recent
> articles as guides in optimizing the simulation parameters. *(DOI: *10.1021/ct900549r
> and *DOI:* 10.1021/jp101581h).
>
> -- Both are using PME for electrostatics and I am planning to do that too
> -- Both have rcoulomb = 1.2 (this value is optimal for CHARMM27 force field
> as mentioned)
> -- In the second paper, they have explicitly assigned rvdw = 1.2
> (this value is also optimized for CHARMM27 force field) and they assigned
> the NS rlist = 1.2 because as I understand, using PME as a coulombtype
> requires rcoulomb to be equal to rlist. I have no problem following up
> until now and it seems that (rlist = rcoulomb = rvdw = 1.2) presents the
> best combination of cut-offs for using (coulombtype = PME and vdwtype =
> cut-off) along with CHARMM27
>
> -- What I can't get is that in the first paper, they mentioned the
> following *"van der Waals interactions were switched off between 1.0 to
> 1.2 nm"*
> *what does that mean in terms of cut-offs and vdwtype?*
> Does that mean *vdwtype = switch*, *vdw_switch* *= 1*, *rvdw = 1.2* ?
>
yes.

> and if this is what is meant, then rlist has to be 0.1-0.3 larger than rvdw
> to accomodate for the size of the charge groups as mentioned in the manual
> and accordingly, we can't keep rcoulomb = 1.2 because rcoulomb must be equal
> to rlist to allow using PME.
>
CHARMM FF doesn't use charge groups. Thus (as far as I understand) this
warning can be ignored.  You still miss a few interactions because
the neighbor-list only contains everything up to 1.2 thus an atom at a
distance just above 1.2 and moves a bit inwards, it is not included until
the next neighbor-list update. But because the interaction is already
switched it is not very critical in my opinion. If you want to avoid this
you can use PME-Switch but this is significant slower.

Roland

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