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

[Davide Mercadante]

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." <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:
>>        <CAD=-
>> 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.
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
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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
>> 
>> ========================================
>> 
>> 
>> 
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