AMBER Archive (2009)

Subject: Re: [AMBER] Changing pH of the system

From: Adrian Roitberg (
Date: Sun Aug 30 2009 - 10:26:01 CDT

Dear Nicholus,
I am confused about your post. You say you want to simulated it at
different pHs and then ask how to regulate the temperature. These are
two different questions.

if you want to do constant pH, read the manual please and one of the
tests examples under amber. It is not trivial to set up, but perfectly
doable. For starters, you will need to recreate your prmtop with the
protonable residues.


nicholus bhattacharjee wrote:
> Dear community,
> I am trying to simulate my protein in different
> pH values. I am using Amber 9. Can anyone tell me how to regulate the
> temperature. Thank you in advance.

                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

Senior Editor. Journal of Physical Chemistry American Chemical Society

University of Florida PHONE 352 392-6972 P.O. Box 118435 FAX 352 392-8722 Gainesville, FL 32611-8435 Email

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