[gmx-users] Metadynamics with Esential Dynamics Sampling

[James Starlight]

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 <jmsstarlight at gmail.com>:
> 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
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> 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 gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> 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 gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>