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
