Re: [AMBER] constant pH equilibration confusion

From: Jason Swails <>
Date: Sat, 19 Jun 2010 16:07:37 -0400


On Sat, Jun 19, 2010 at 3:59 PM, Sangita Kachhap <>wrote:

> Ya I have seen the tutorial for simulation of DNA in implicit solvant

There is no tutorial for "constant pH" simulations specifically, though it
is not much different than other implicit solvent simulations

> there is relaxing the DNA before MD simulation at tempi = 300.0, temp0 =
> 300.0.
> But actualy in one of the reply of my mail I got about heating and
> equilibration
> so thats why I have confusion.
> For constant pH simulation I am donig the following step is it correct or
> not?
> 1)minimization:
> a)minimization of hydrogen only (by mistake I my earlier mail I have wrote
> that i hvae apply restraint on hydrogen).

I would not minimize just the hydrogens. The hydrogen distances won't
change due to SHAKE, so I don't think you gain much by this step.

> b)minimization of whole system

This seems to me to be the only minimization you really need. It doesn't
need to be long, either, since it's just relaxing bad contacts. You may
also add restraints to the backbone atoms to prevent any kind of major
distortion of secondary structure.

> 2)heating (now which I will not do) and equilibration at tempi = 300.0,
> temp0 =
> 300.0

You certainly need to heat. And apply restraints to the backbone atoms like
I've suggested, most likely. I have, on occasion, seen the entire protein
unravel during heating, though that could be due to a couple bugs that were
patched up in the constant pH code (make sure you apply all of these bug
fixes! 47 for amber9 and 25 for amber10). In any case, I think it's a good
idea to apply some restraints to the backbone while you're heating and

> 3)production run.

You can take off all restraints here and just run freely.

Good luck!

> >> Now I have to euqilibrat it with heating 0 - 300K.
> >
> > Have you looked at the tutorials?
> >
> > Bill
> >
> > _______________________________________________
> > AMBER mailing list
> >
> >
> >
> >
> Sangita Kachhap
> _______________________________________________
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sat Jun 19 2010 - 13:30:03 PDT
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