[gmx-users] energy perturbation

Maik Goette mgoette at mpi-bpc.mpg.de
Wed Jan 9 09:23:18 CET 2008


If I'm not totally wrong, a howto setup a free energy perturbation 
topology is written in the manual. Additionally David and others brought 
up several links to tutorials here in the mailing list. So simply use 
the search function and read the manual.

A perturbed atom entry for OPLSAA ( and in fact for all others) looks 
like this:

#ID  TypeA         Resn  Resid  Atom  hargegr. ChargeA   Mass A   Type B 
   Charge B  Mass B

12  opls_224B      2    TRP     CA      3       0.14     12.011 
opls_223B 0.08 12.011

A general tip: Before proceeding, inform yourself about the different 
free energy calculation methods and how they are used in GROMACS. 
Especially have a look into "softcore" and be aware of using it JUST for 
vdw morphing...


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Farzad Molani wrote:
> Hi Mark
> I read the manual and I used umabrella sampling and I got a curve for 
> pmf but now I want pmf by energy perturbation that I want to sure about 
> my curve that I got by umbrella sampling.
> my question is about .itp file and how do I create.
> thank you very much.
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