Hi
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...
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.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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