R: [gmx-users] Conformational sampling

[Spitaleri Andrea]

Dear Nisha,
have look to the plumed plugin in gromacs:

http://merlino.mi.infn.it/~plumed/PLUMED/Home.html

you can perform US and Metadynamics calculations.

Hope it helps

and
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Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://sites.google.com/site/andreaspitaleri/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
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________________________________________
Da: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] per conto di nishap.patel at utoronto.ca [nishap.patel at utoronto.ca]
Inviato: venerdì 6 agosto 2010 17.08
A: gmx-users at gromacs.org
Oggetto: [gmx-users] Conformational sampling

Hello,

     I would like to do conformational sampling for my simulation of
one glycine in its zwitterionic form in water and obtain a PMF curve
to see if the system is equilibrated and that all possible torsions
are covered for my 100ns run. I am not sure how to approach this
issue. Is there a tutorial I can follow? Do I need to do umbrella
sampling and use WHAM to extract PMF?

I would appreciate some help!

Thanks.
Nisha P.

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