Thanks for the suggestion.
Also, I was wondering how one can get the time profile of the irreversible
work from the gromacs pull-code out put . From constant pulling-rate SMD, we
get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying
the the value from pullx.xvg and value from pullf.xvg will provide the work .
Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate
multiplied by time ?
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: Sanku M <msank...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
Sent: Thursday, November 3, 2011 9:27 PM
Subject: Re: [gmx-users] Steered MD in reverse direction?
Sanku M wrote:
> Hi,
> I am performing steered Molecular dynamics simulation to pull a molecule
>out of a complex. I am using gromacs 4.5.4 to perform the constant rate
>pulling..I have done the steered MD simulation in a particular direction i.e
>hav pulled the molecule out of complex.
> But, to check the convergence/hysterisis of the pulled path way, I would like
> to perform the same steered MD in reverse direction i.e push the molecule
> back into the complex. But, I was wondering, to perform the backward steered
> MD, how should I modify the .mdp parameters? Should I make the pull_rate1
> negative or switch the pull_group0 and pull_group1 ? Any help will be
> appreciated.
>
Use a negative pull rate. But simple pulling like this can be difficult;
you're now trying to hit a moving target. A slight rotation of the protein can
render the whole simulation junk - your pulled molecule may smack into some
undesired location.
-Justin
> The following is the part of the pull-code parameter I am using:
> ; Pull code
> pull = umbrella
> pull_geometry = distance ; simple distance increase
> pull_dim = N N Y
> pull_start = yes ; define initial COM distance > 0
> pull_ngroups = 1
> pull_group0 = Mol_A
> pull_group1 = Mol_B
> pull_rate1 = 0.0025 ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 1000 ; kJ mol^-1 nm^-2
>
> Sanku
>
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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