Thank you Jason and Hannes! I guess by putting the following in my NAMD
.conf file I can run a protein-membrane simulation with the lipid11 or
lipid14 ff without carbonhydrates. Lipid11/14 does not use different
scaling factors than the amber ff, right?
exclude scaled1-4
1-4scaling 0.8333;# must be 1/scee, where scee is the
electrostatic scaling factor in AMBER
scnb 2.0 ;# VDW 1-4 scaling factor, required for AMBER
ff (although the default value is the same)
On 4 June 2014 13:07, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
> On Tue, 3 Jun 2014 17:58:11 -0400
> Jason Swails <jason.swails.gmail.com> wrote:
>
> > He didn't know
> > > exactly though what happens. Aren't these parameters defined
> > > explicitly in the .prmtop file so that NAMD could know how to
> > > compute the vdW and electrostatics correctly, or does the code
> > > override them?
> > >
> >
> > My guess is that NAMD ignores the SCEE_SCALE_FACTOR and
> > SCNB_SCALE_FACTOR sections of the prmtop and simply uses scee and
> > scnb as input by the user. But that may have changed in recent
> > versions.
>
> I have just tested this with today's CVS version of namd and it still
> ignores those flags.
> --
> Scanned by iCritical.
>
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--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Jun 04 2014 - 04:30:02 PDT
