Hi Rajeswari, try this really interesting work done by De Simone et al. and published recently on PNAS.
http://www.pnas.org/content/109/18/6951.full Hope this helps. Cheers, Davide Davide Mercadante Ph.D. School of Chemical Sciences The University of Auckland Auckland New Zealand On 3/11/2012, at 6:32 PM, Rajeswari A. wrote: > Thank you Rama and Justin for ur kind reply. > > @Justin: May i request you to kindly direct me to some references of > multiple protein simulation in a box using standard MD? And i have seen the > tutorial about multi protein simuation is under development. May i know > when can we expect it to be ready? Once again i thank you for ur reply. > > @Rama : I want to study protein aggregation. > > Thank you, > Rajeswari. > > > >> Message: 1 >> Date: Fri, 2 Nov 2012 15:22:03 +0530 >> From: "Rajeswari A." <[email protected]> >> Subject: [gmx-users] Multiple protein simulations in a box >> To: [email protected] >> Message-ID: >> < >> caozjml_pm6n_lkyx36_jfll90h-deia2owrrdouj_1mthet...@mail.gmail.com> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Dear Gromacs Users, >> I want to simulate multiple number of proteins in a box. I am very confused >> in choosing what MD method will be useful to solve my problem. Can i do it >> with regular molecular dynamics simulations? I am not sure whether >> diffusion of solutes are taken care in standard MD. or should i opt >> brownian dynamics for this purpose? Is there any special method where i can >> do simulate multiple proteins in a box? >> >> Thank you. >> Rajeswari. >> >> >> Message: 3 >> Date: Fri, 2 Nov 2012 15:34:56 +0530 >> From: rama david <[email protected]> >> Subject: Re: [gmx-users] Multiple protein simulations in a box >> To: Discussion list for GROMACS users <[email protected]> >> Message-ID: >> <CAD=- >> [email protected]> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Dear Rajeswari, >> May I ask you why you want to do the multiple protein simulation.?? >> Please mention the purpose clearly, otherwise it is hard to understand >> what you are doing and what you need???, >> >> With best wishes and Regards, >> Rama David >> >> >> On Fri, Nov 2, 2012 at 3:22 PM, Rajeswari A. <[email protected] >>> wrote: >> >>> Dear Gromacs Users, >>> I want to simulate multiple number of proteins in a box. I am very >> confused >>> in choosing what MD method will be useful to solve my problem. Can i do >> it >>> with regular molecular dynamics simulations? I am not sure whether >>> diffusion of solutes are taken care in standard MD. or should i opt >>> brownian dynamics for this purpose? Is there any special method where i >> can >>> do simulate multiple proteins in a box? >>> >>> Thank you. >>> Rajeswari. >>> -- >>> 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 >>> >> >> >> ------------------------------ >> Message: 5 >> Date: Fri, 02 Nov 2012 06:24:29 -0400 >> From: Justin Lemkul <[email protected]> >> Subject: Re: [gmx-users] Multiple protein simulations in a box >> To: Discussion list for GROMACS users <[email protected]> >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> >> On 11/2/12 5:52 AM, Rajeswari A. wrote: >>> Dear Gromacs Users, >>> I want to simulate multiple number of proteins in a box. I am very >> confused >>> in choosing what MD method will be useful to solve my problem. Can i do >> it >>> with regular molecular dynamics simulations? I am not sure whether >>> diffusion of solutes are taken care in standard MD. or should i opt >>> brownian dynamics for this purpose? Is there any special method where i >> can >>> do simulate multiple proteins in a box? >>> >> >> You can use standard MD methodology. Most of the literature I have seen >> involving multiple proteins does. >> >> -Justin >> >> -- >> ======================================== >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> >> > -- > 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
