[gmx-users] negative values of force

[Justin A. Lemkul]

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 <psamrat10 at yahoo.com>
> *To:* jalemkul at vt.edu; Discussion list for GROMACS users 
> <gmx-users at gromacs.org>
> *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 <jalemkul at vt.edu>
> *To:* Gromacs Users' List <gmx-users at gromacs.org>
> *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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>  > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
>  > *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
> 
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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

========================================