[gmx-users] PLUMED plugin in gromacs for protein system

[andrea spitaleri]

Hi Neeru,
this is an issue for the plumed mailing list. Try there.

http://sites.google.com/site/plumedweb/home

regards

and

On 04/19/2012 07:16 AM, neeru sharma wrote:
> Dear gromacs users,
>
> I am a gromacs user and need some help regarding the implementation of PLUMED plugin in gromacs.
>
> I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP using Gromacs which is a 166
> residue protein+mg+GTP/GDP complex. I have already carried out classical MD simulation for the
> Protein-Mg-GDP complex. Then, I replaced GDP with GTP in the complex and now have to analyse the
> structural changes in the Protein-Mg-GTP complex during the simulation. I tried to perform classical
> MD simulation for the Protein-Mg-GTP complex too. But, as GDP to GTP state transition is a
> millisecond time-scale event, through classical MD, it seems practically impossible to achieve this
> time-scale transition.
>
>
> I was looking for the methods available in gromacs that can accelerate this event. I came across the
> PLUMED plugin. I have some queries with respect to the above matter.
>
> 1) Can we manually specify simulation length when performing the simulation, that we want to finish
> the simulation in the given specified time duration?
> 2) How can we specify reaction coordinates (Eg: The RMSD with the desired output state, Specific
> H-bonding or distance pattern etc) for the simulation, as I already have the crystal structure
> available with me for the Protein-Mg-GTP complex (output state desired to be achieved with the
> simulation).
>
> As, I am new to gromacs, can you please help me regarding the above mentioned matter, usage of
> plumed plugin for protein system and how it can be approached with my system?
>
>
> Any help will be highly appreciated.
>
> Thanks in advance
>
> Regards,
>
> Neeru

-- 
-------------------------------------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute c/o Raffaele Scientific Institute
Biomolecular NMR Laboratory Dibit2 Basilica 3A2
Via Olgettina 58
20132 Milano
Italy
Tel: 0039-0226434348
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
http://www.linkedin.com/in/andreaspitaleri
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