[gmx-users] Rupture force definition

Tue Jun 4 06:54:30 CEST 2019

Thanks Justin,

I want to see the change statistically by using same parameter (velocity
and same spring constant)
Hence, I think it will be better to pull the same system  by choosing its
different conformation.
 Eg. I  had taken the the last conformation of production md ( 50 ns) for
pulling.  Then in order
to see the differences we can take conformation at 40th ns and apply the
pull with same parameter
(Same velocity and same spring constant ).

On Mon, May 20, 2019 at 6:07 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/17/19 6:15 AM, Rakesh Mishra wrote:
> > Dear Justin
> >
> > After long time again I want to ask one question.
> > If suppose I want to repeat the same production
> > simulation ( final md simulation) for different seeds,
> > then how to do. Because as from the knowledge of
> > gromacs there is no manual way to put different seeds
> > in the .mdp files.
>
> gen-seed gives you different starting velocities. If you want to perform
> independent simulations they need to either start from (1) different
> velocities, (2) different conformations, or (3) different pull vectors.
>
> -Justin
>
> >
> > On Mon, Jun 25, 2018 at 7:27 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 6/25/18 8:48 AM, Rakesh Mishra wrote:
> >>> Dear Justin.
> >>>
> >>> I have observed one thing that during pulling (Constant velocity
> pulling
> >> )
> >>> of dsDNA/dsRNA ( globally say Nucleic acid ) along helical direction,
> we
> >>> observe that in the force/time .xvg file, some time force value  is +ve
> >> and
> >>> some time force value is -ve. So why it happens. In my thinking it
> should
> >>> always be +ve.
> >> Free energy surfaces are rugged. Some intermediate conformations may
> >> result in local free energy wells.
> >>
> >> -Justin
> >>
> >>> On Mon, Jun 11, 2018 at 5:37 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> >>>
> >>>> On 6/8/18 2:52 AM, Rakesh Mishra wrote:
> >>>>
> >>>>> Dear Justin .
> >>>>> I have  two query
> >>>>>
> >>>>> 1-What can be the optimized value of rate can be taken
> >>>>> for pulling of  dsDNA/dsRNA using gromacs format where solvent is
> >> aqua.
> >>>>>    From your umbrella sampling manual,  rate is very high like (0.01
> >> nm/ps),
> >>>>> which is equal to 0.0001Angstrom/fs.
> >>>>>
> >>>> You'll note in the SI we tested lower values and achieved the same
> >>>> outcome, so you need to test a few to be sure that whatever pull rate
> >> you
> >>>> impose does not introduce artifacts. There is no way, a priori, to
> know
> >>>> what an "optimized" rate would be. That term also has multiple
> >>>> interpretations.
> >>>>
> >>>> 2- In pulling mdp file no random seed is discussed. But if we want to
> >>>>> obtain 2 or 3 different trajectory during
> >>>>>         pulling ( of the same system ) for  different seed, then how
> to
> >> give
> >>>>> different seed in pulling  mdp file.
> >>>>>
> >>>>> Note -  In my thinking in gromacs, gen_seed  = -1 is default value.
> >> And
> >>>>> it
> >>>>> comes , when NVT is applied ( where
> >>>>>                 velocity generation is allowed, to achieve required
> >>>>> temperature through maxwell distribution ). But in case of pulling,
> >> where
> >>>>> no velocity
> >>>>>                 generation is allowed . Then how to calculate
> different
> >>>>> pulling simulation of the same system for different seeds.
> >>>>>
> >>>> One does not supply a new random seed when doing a continuation of a
> >> run.
> >>>> If you want to start new simulations in each window or in multiple
> >>>> replicates of a run, then use "gen_seed = -1" to get a completely
> random
> >>>> seed based on the process ID.
> >>>>
> >>>>
> >>>> -Justin
> >>>>
> >>>> --
> >>>> ==================================================
> >>>>
> >>>> Justin A. Lemkul, Ph.D.
> >>>> Assistant Professor
> >>>> Virginia Tech Department of Biochemistry
> >>>>
> >>>> 303 Engel Hall
> >>>> 340 West Campus Dr.
> >>>> Blacksburg, VA 24061
> >>>>
> >>>> jalemkul at vt.edu | (540) 231-3129
> >>>> http://www.thelemkullab.com
> >>>>
> >>>> ==================================================
> >>>>
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> >>>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Virginia Tech Department of Biochemistry
> >>
> >> 303 Engel Hall
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
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>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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-- 

*With Best-Rakesh Kumar Mishra  (RA)*

*Dr. D. S. Kothari Fellow.School of Computational *
*& Integrative Sciences, JNU.*
*Phone n. +91 9473662491, +918777496532*