On 11/9/13 4:16 PM, rajat desikan wrote:
Hi Justin,
I take it that both the sets of parameters should produce identical
macroscopic quantities.
For the GPU, is this a decent .mdp?
cutoff-scheme = Verlet
vdwtype = switch
rlist = 1.2
;rlistlong = 1.4 NOT USED IN GPU...IS THIS
OK?
rvdw = 1.2
;rvdw-switch = 1.0 NOT USED IN GPU...IS THIS OK?
coulombtype = pme
DispCorr = EnerPres
rcoulomb = 1.2
I have no basis for saying whether or not it will produce correct results. I
have never tested this force field on GPU with the Verlet scheme. My biggest
concern is with the treatment of van der Waals interactions, and I have not used
the Verlet scheme enough to understand what it is doing and how it will treat
the interactions that should be switched. If someone else can comment, that
would be useful to me, as well!
Test carefully and please report back. A comparison between CPU and GPU would
be very valuable.
-Justin
On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5012351...@n6.nabble.com> wrote:
On 11/7/13 11:32 PM, Rajat Desikan wrote:
Dear All,
The setting that I mentioned above are from Klauda et al., for a POPE
membrane system. They can be found in charmm_npt.mdp in lipidbook (link
below)
http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html
Is there any reason not to use their .mdp parameters for a
membrane-protein
system? Justin's recommendation is highly valued since I am using his
forcefield. Justin, your comments please
Careful now, it's not "my forcefield." I derived only a very small part
of it :)
To summarize:
Klauda et al., suggest
rlist = 1.0
rlistlong = 1.4
rvdw_switch = 0.8
vdwtype = Switch
coulombtype = pme
DispCorr = EnerPres ;only usefull with reaction-field
and pme or pppm
rcoulomb = 1.0
rcoulomb_switch = 0.0
rvdw = 1.2
Justin's recommendation (per mail above)
vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2
The differences between these two sets of run parameters are very small,
dealing
mostly with Coulomb and neighbor searching cutoffs. I would suspect that
any
difference between simulations run with these two settings would be
similarly
small or nonexistent, given that rcoulomb is a bit flexible when using
PME. The
value of rlist is rarely mentioned in papers, so it is good that the
authors
have provided the actual input file. Previous interpretation of CHARMM
usage
generally advised setting rcoulomb = 1.2 to remain consistent with the
original
switching/shifting functions. That setting becomes a bit less stringent
when
using PME.
-Justin
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