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
