A few comments here. First, gamma_ln!=0 is an error when ntt!=3 unless I'm
mistaken, so the default gamma_ln needs to either be 0 or dependent on
ntt=3. However, there *is* a use-case for ntt = 3 and gamma_ln = 0 -- it's
a good test for testing and validation. In this case, the Langevin
integrator should be equivalent to the standard integrator.
+1 for the change in principle, though.
All the best,
Jason
On Wed, Mar 9, 2016 at 11:13 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I agree that an error might be better than changing it away from what the
> input says. if it does that, we should make it the default so it's
> documented that way.
>
> On Wed, Mar 9, 2016 at 10:56 AM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
>
> > > Didn't the code use to quit with an error telling you gamma_ln needed
> to
> > be set if you set ntt=3 and didn't change it. Did this change at some
> point?
> >
> > >From mdin_ctrl_dat.F90 in pmemd
> >
> > gamma_ln = 0.d0 !Default is zero but if ntt=3 we set it to 1.0d0
> >
> > if (gamma_ln .gt. 0.d0 .and. ntt .ne. 3) then
> > write(mdout, '(a,a)') error_hdr, 'ntt must be 3 if gamma_ln > 0!'
> > inerr = 1
> > end if
> >
> > if ( ntt == 3 .and. ntb == 2) then
> > !Require gamma_ln > 0.0d0 for ntt=3 and ntb=2 - strange things happen
> > !if you run NPT with NTT=3 and gamma_ln = 0.
> > if ( gamma_ln <= 0.0d0 ) then
> > write(mdout,'(a,a)') error_hdr, 'gamma_ln must be > 0 for ntt=3
> with
> > ntb=2.'
> > inerr = 1
> > end if
> > end if
> >
> > So it requires it for NTP runs and the comment implies it is set to 1.0
> > for ntt=3 but never actually is. So close to what you want...
> >
> >
> > > On Mar 9, 2016, at 07:55, Carlos Simmerling <
> carlos.simmerling.gmail.com>
> > wrote:
> > >
> > > Sorry that wasn't clear - I support changing it.
> > > On Mar 9, 2016 9:34 AM, "Carlos Simmerling" <
> carlos.simmerling.gmail.com
> > >
> > > wrote:
> > >
> > >> I would agree, users could I tend to turn it on (ntt) but have it not
> > >> really turn on....
> > >> On Mar 9, 2016 9:33 AM, "Adrian Roitberg" <roitberg.ufl.edu> wrote:
> > >>
> > >>> Hi
> > >>>
> > >>> The default for gamma_ln for langevin thermostat (ntt=3) is =0, which
> > >>> basically means constant energy. Obviously, when you use shake and a
> > >>> dt=0.002 energy is not really conserved, so there is trouble.
> > >>>
> > >>> Should we keep it as 0 or change it to something small but useful,
> > like 1?
> > >>>
> > >>> adrian
> > >>>
> > >>> --
> > >>> Dr. Adrian E. Roitberg
> > >>> Professor.
> > >>> Department of Chemistry
> > >>> University of Florida
> > >>> roitberg.ufl.edu
> > >>> 352-392-6972
> > >>>
> > >>>
> > >>> _______________________________________________
> > >>> AMBER-Developers mailing list
> > >>> AMBER-Developers.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> > >>>
> > >>
> > > _______________________________________________
> > > AMBER-Developers mailing list
> > > AMBER-Developers.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Wed Mar 09 2016 - 10:00:03 PST
