[gmx-users] Re: Multiple protein simulations in a box

[Rajeswari A.]

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." <rajeswari.biotech at gmail.com>
> Subject: [gmx-users] Multiple protein simulations in a box
> To: gmx-users at gromacs.org
> Message-ID:
>         <
> CAOzJmL_PM6N_LKyX36_JFLL90H-DEia2OWrrdOUJ_1mTHeT++Q at 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 <ramadavidgroup at gmail.com>
> Subject: Re: [gmx-users] Multiple protein simulations in a box
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
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> SYHuM_rLGNm1Ys4-shpqh_8yqkG4mH7Ed164ngOzM0-hLA at mail.gmail.com>
> 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. <rajeswari.biotech at gmail.com
> >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.
> > --
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>
> ------------------------------
> Message: 5
> Date: Fri, 02 Nov 2012 06:24:29 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Multiple protein simulations in a box
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <50939F5D.2080805 at vt.edu>
> 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
>
> ========================================
>
>
>