Hey Jason
When I add the leaprc.constph for creating a prmtop/inpcrd file ,
frcmod.constph gets loaded. So I'm guessing the improper terms are added
when I create my prmtop file.
Rahul Ramesh
Masters Student
Department of Chemical Engineering
University of Michigan Ann Arbor
(+1 734-680-4453)
On Fri, Oct 16, 2015 at 7:57 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, Oct 15, 2015 at 11:43 PM, Rahul Ramesh <raramesh.umich.edu> wrote:
>
> > Hello
> > I am simulating a polymeric chain in which COOH is my titrating group. I
> > have a -3mer system in which one of the monomers has the titrating group
> > attached in the form of a succinate group. I understand that two
> hydrogens
> > must be attached to each of the carboxylic oxygens to account for the
> ghost
> > proton. In my case, the protons are overlapping while doing the CpHMD
> and I
> > get a warning (vlimit exceeded along with extremely high and fluctuating
> > temperatures ). Is there a technique as to when to add these three extra
> > protons to the carboxylic oxygen. I added it after my Gaussian geometry
> > optimization. Should the geometry optimization be done with these 4
> protons
> > attached to the oxygens. or Is there any other reason why vlimit can be
> > exceeded during the constant pH simulation. When I set my ncnstph as a
> very
> > high value say 10000, this problem does not arise.
> >
>
> I recommend having a look at the residue definition of AS4 and GL4 along
> with the parameters that were introduced specifically to prevent these
> ghost hydrogen atoms from rotating around. Improper torsional restraints
> were added *specifically* to prevent this kind of thing from happening.
>
> Did you add these same improper terms? If you do, does it fix the problem?
> (You can find the constant pH parameters in
> $AMBERHOME/dat/leap/parm/frcmod.constph.)
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 16 2015 - 11:00:04 PDT
