[gmx-users] Steered MD in reverse direction?

Sanku M msanku65 at yahoo.com
Fri Nov 4 18:28:46 CET 2011

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 <jalemkul at vt.edu>
To: Sanku M <msanku65 at yahoo.com>; Discussion list for GROMACS users <gmx-users at 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.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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