[gmx-users] Metadynamics with Esential Dynamics Sampling

[James Starlight]

Thanks for advide!

I've already posted topic on their board! But at presence I mostly
intresting in the Spiwok's technique ( whjich is the just md-run as
well as make-edi patch ).

James

2012/12/22 Spitaleri Andrea <spitaleri.andrea at hsr.it>:
> Hi,
>
> I suggest you to visit the plumed webpage and ask to the mailing list.
>
>
> http://www.plumed-code.org/
>
>
> best
>
> and
>
> Andrea Spitaleri PhD
> Dulbecco Telethon Institute
> Center of Genomics, BioInformatics and BioStatistics
> Basilica San Raffaele, 3P 34R
> Via Olgettina 58
> 20132 Milano (Italy)
> http://sites.google.com/site/andreaspitaleri/
> www.biomolnmr.org
> 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
> EDS ?
>
> Thanks for help,
>
> James
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