Re: [AMBER] Question on applying restraints in absolute dG calculations with TI in Amber 10

From: <steinbrt.rci.rutgers.edu>
Date: Thu, 25 Feb 2010 05:15:13 -0500 (EST)

Hi Samuel,

> I modified thermo_int.f, in the way you told me, ran a shorter
> simulation and here is a part of the output

ok, I tried the same here and it looks the way it should. I have updated
the manual for your suggestion and fixed the code and test cases for the
new release. Thanks again for spotting this, it was a stupid mistake on my
side.

> You better put together a bug fix.

I have made one and attached it. What you did change should have the same
effect, but feel free to try it out.

Just for sake of completeness: What I said before about non-linear dvdl
contributions making dvdl not equal to V0-V1 is correct, but this term is
explicitly added to the VDWAALS energy internally, so that total dvdl
should indeed be equal to VDWAALS in your case.

Kind Regards,

Thomas

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Feb 25 2010 - 02:30:02 PST
Custom Search