R: [gmx-users] Metadynamics with Esential Dynamics Sampling

Spitaleri Andrea spitaleri.andrea at hsr.it
Sat Dec 22 09:23:12 CET 2012


I suggest you to visit the plumed webpage and ask to the mailing list.




Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
Basilica San Raffaele, 3P 34R
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348
Fax: 0039-0226434153
Da: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] per conto di James Starlight [jmsstarlight at gmail.com]
Inviato: venerdì 21 dicembre 2012 21.09
A: Discussion list for GROMACS users
Oggetto: [gmx-users] Metadynamics with Esential Dynamics Sampling

Dear Gromacs Users!

Recently I've found algorithm for calculation of the free-energy along
essential subspaces proposed by Spiwok. I wounder to know more about
technical details of that algorithm.

Earlier I've used Essential Dynamics sampling for simulation of
membrane receptors. In that case I've created run edi files as well as
run my simulations with Gromacs 4.5.5 on 100 nodes cluster. Has your
algorithm compatibility with that Gromacs version ? Must I patch
gromacs run files on both work-station ( where system preparation as
well as generation of edi files are performed) as well as on cluster
(where calculation via md_run) are performed ?

Also I've found another possibility of using metadynamics in GROMACS (
e.g PLUMED). Have anybody try to use it? Did it compatible with the

Thanks for help,

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