Samrat Pal wrote:
Hi Justin,
I the pullf.xvg file also, some values are negative. I am giving below
the pull code -
pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = yes
pull_ngroups = 1
pull_group0 = freeze
pull_group1 = pull
pull_rate1 = 0.01
pull_k1 = 1000
I have given pull_dim Y Y Y as I am not pulling in a particular
direction. Is it right?
You can answer that question yourself by looking at the dX, dY, and dZ entries
in pullx.xvg.
As far as the negative values go, there's no way to assess whether that's
necessarily right or wrong. If you produce a configuration that is equally
influenced by the pulling force and other forces in the system, it may oscillate
between positive and negative.
-Justin
------------------------------------------------------------------------
*From:* Samrat Pal <[email protected]>
*To:* [email protected]; Discussion list for GROMACS users
<[email protected]>
*Sent:* Sat, August 14, 2010 11:00:37 AM
*Subject:* Re: [gmx-users] negative values of force
Thanks a lot.
Best
Samrat
------------------------------------------------------------------------
*From:* Justin A. Lemkul <[email protected]>
*To:* Gromacs Users' List <[email protected]>
*Sent:* Sat, August 14, 2010 10:50:05 AM
*Subject:* Re: [gmx-users] negative values of force
Samrat Pal wrote:
> (1) I have got the pull.xvg file from the simulation. But there the
data resolution is very high e.g after every 2 ps. But I don' need that.
So, I tried to create a new .xvg file with lower resolution of data e.g.
after every 50 ps. So, I used the g_traj command.
>
Then you should have chosen a better value of pull_nstfout. Otherwise,
you can write a simple script to parse out data at more useful intervals.
> (2) So, there is no error in getting the negative value of force, right?
>
No. Force is a vector quantity. Depending on the direction of motion
of a particular atom, the force may be moving it in a positive or
negative direction. This is very fundamental physics.
> (3) I have also created a dist.xvg file by applying g_dist command.
Can I use force.xvg (created by g_traj) and dist.xvg (created by g_dist)
files to get force vs. extension profile?
Again, the actual pull output (pullx.xvg) should be a suitable match for
your pullf.xvg data.
-Justin
> Best
> Samrat
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <[email protected] <mailto:[email protected]>>
> *To:* Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
> *Sent:* Sat, August 14, 2010 10:34:25 AM
> *Subject:* Re: [gmx-users] negative values of force
>
>
>
> Samrat Pal wrote:
> > Dear All,
> > I have pulled a protein by keeping n-terminus fixed
and pulling the c-terminus. I tried to extract the force.xvg profile
from the .trr file by the following command -
> >
>
> If you've applied the pull code, is there some reason that the
pullf.xvg file does not contain the information you're looking for?
>
> > g_traj -f traj.trr -s pull.tpr -of force.xvg
> >
> > But in the force.xvg profile I am getting both positive and
negative values of force. What does it mean? Please suggest.
>
> Simple Newtonian physics. g_traj is extracting instantaneous forces
on the constituent atoms, as stored in the .trr file, so all effects are
considered - pull force, intermolecular collisions, etc.
>
> -Justin
>
> > Samrat
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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>
-- ========================================
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
========================================
-- gmx-users mailing list [email protected]
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--
========================================
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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