[gmx-users] negative values of force

[Samrat Pal]

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?




________________________________
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>
> *To:* Discussion list for GROMACS users <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> | (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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