[gmx-users] Re: gmx-users Digest, Vol 13, Issue 71

[Anil Kumar]

>    4. dynamic search and simulated annealing
>       (UCT Staff Member - Jackson)
>

Dear Jackson,

As, i understand your problem is, to do simmulated annealing on each
structures which is the output of the previous cylcle and by this way you
want to generate 100 structures.
So for this you have to run one cycle and then automate the commands in a
shell script file which will convert previous high.gro into input2.pdb and
run the second cuycle and so on.
Recently one paper has come from my supervisor's Research group i.e.,

Ramakrishnan, V., Ranbhor, R., & Durani, S. (2005) Biopolymers 78, 96-105

You just go through this paper, you will get the answer how to do it.

o.k.
bye
cheers.

anil

ANIL KUMAR(Research Scholar)
Bio-Organic Lab No-336(2nd Floor)
Dept. of Chemistry,
I.I.T.Bombay,Powai,
Mumbai-400076 (INDIA)
Ph. No.-022-25764780(Lab),
        022-25764168(Lab)
-----------------------------------------
Residence:-
Hostel#1,Room#297,IIT Bombay,Powai,
Mumbai-400076,Ph.No.:-022-56036275(Hostel),
Mobile:-09819638547
--------------------------------------------------
"Education is a progressive discovery of our ignorance"

- Will Durant
------------------------------------------


> Message: 4
> Date: Thu, 26 May 2005 08:36:46 +0200
> From: UCT Staff Member - Jackson <Jackson at SCIENCE.uct.ac.za>
> Subject: [gmx-users] dynamic search and simulated annealing
> To: gromacs <gmx-users at gromacs.org>
> Message-ID: <42956E7E.5B45FF2F at SCIENCE.uct.ac.za>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Users
> I want to use high temperature molecular dynamics to search
> conformational space.  The protcol is to do a long run and collect 100
> structures on the way.  I then need to do simulated annealing on each of
> those 100 structures.  Simulated annealing on one structure is easy but
> how do I get mdrun to repeat the process on each of the structures in
> the trajectory?
> Thanks
> Graham
> --
> Professor Graham E. Jackson
> Department of Chemistry
> University of Cape Town
>
> Tel: (021) 6502531
> Fax: (021) 6897499
>
>
> Mail: ygmu at ntu.edu.sg
>
>> -----Original Message-----
>> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org]
>> On Behalf Of UCT Staff Member - Jackson
>> Sent: Thursday, May 26, 2005 2:37 PM
>> To: gromacs
>> Subject: [gmx-users] dynamic search and simulated annealing
>>
>> Dear Users
>> I want to use high temperature molecular dynamics to search
>> conformational space.  The protcol is to do a long run and collect 100
>> structures on the way.  I then need to do simulated annealing on each
> of
>> those 100 structures.  Simulated annealing on one structure is easy
> but
>> how do I get mdrun to repeat the process on each of the structures in
>> the trajectory?
>> Thanks
>> Graham
>> --
>> Professor Graham E. Jackson
>> Department of Chemistry
>> University of Cape Town
>>
>> Tel: (021) 6502531
>> Fax: (021) 6897499
>> _______________________________________________
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>> gmx-users at gromacs.org
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>
>


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