by the way it's also interesting to me if there are any other possible ways to obtain representation of the free energy surfaces in the essential coordinates subspace ? Might the methods like Ubrella sampling ( with applied PMF in the pulling direction along selected eigenvector ) or flooding (already implemented in the EDS) ?
James 2012/12/22, James Starlight <[email protected]>: > 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 <[email protected]>: >> 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: [email protected] [[email protected]] per >> conto di James Starlight [[email protected]] >> 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 >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
