[gmx-users] Re: gmx-users Digest, Vol 96, Issue 146

[Matthew Zwier]

Hi Neeru,

No, unfortunately I don't know much about conformational flooding, or
PLUMED.  My own research has focused more on the path sampling family.
 PLUMED questions come up here and there on this list, so it seems
like there are at least a few other people using it.

MZ

On Thu, Apr 19, 2012 at 1:12 AM, neeru sharma <neeru.bioinfo at gmail.com> wrote:
>
>
> Hi Matthew,
>
> Thanks for your response. I will definitely look into the NEB method,
> suggested by you. By the way, do you have any idea about Flooding approach
> or the PLUMED plugin in gromacs for performing such simulations?
>
> Thanks in advance.
>
> Neeru.
>
>
>>
>> Hi Neeru,
>>
>> Any number of enhanced sampling techniques might do this, but weighted
>> ensemble, forward flux sampling, milestoning, and transition path
>> sampling (all described in (Zwier, M. C.; Chong, L. T. Current Opinion
>> in Pharmacology 2010, 10, 745–752.) and the nudged elastic band method
>> (Bergonzo, C., Campbell, A.J., Walker, R.C., Simmerling, C., "A
>> Partial Nudged Elastic Band Implementation for Use with Large or
>> Explicitly Solvated Large Systems", Int. J. Quant. Chem., 2009, 109,
>> 15, 3781-3790) come to mind.  The nudged elastic band method, in
>> particular, might be a good place to start, since you have initial and
>> final structures.
>>
>> To my knowledge, none of these is implemented directly within GROMACS,
>> but all could be implemented using GROMACS as a dynamics backend.
>> (NEB
>>
>> On Wed, Apr 18, 2012 at 2:26 AM, neeru sharma <neeru.bioinfo at gmail.com>
>> wrote:
>> > Dear Gromacs users,
>> >
>> >
>> > I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP
>> > using
>> > Gromacs. 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 already have the crystal structure available with me for the
>> > Protein-Mg-GTP complex.
>> > As, I am new to gromacs, can anybody suggest me any method to perform
>> > this
>> > transition using some accelerated molecular dynamics method available
>> > with
>> > gromacs and how it can be performed for my system?
>> >
>> >
>> > Any help will be highly appreciated.
>> >
>> > Thanks in advance
>> >
>> > -----
>> > Neeru Sharma,
>> > Pune (India)
>>
>>
>>
>> ------------------------------
>
>
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