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
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Received on Fri Oct 16 2015 - 05:00:04 PDT
