[gmx-users] The pullf.xvg and pullx.xvg files

[Justin Lemkul]

On 6/24/15 9:20 AM, Laura Tociu wrote:
> Dear Justin,
>
> Thanks for the reply! Yeah, I understand how the pulling works now. The
> forces at time t=0 are not zero, though. There are huge forces such as -270
> or even -1700 kj/mol/nm acting on my pull group at time t=0.  What do you
> believe could be the cause of that? And why is there a /nm in that force? I
> mean, isn't the force per nm (force constant) of the spring always 1000
> kj/mol/nm, but the actual force adopts various different values as time
> goes by?
>

The force constant is in kJ/mol/nm^2 (same as all bonded force constants). 
Force is kJ/mol/nm because force is the negative derivative of potential with 
respect to position.  You can also convert this rather easily to pN or some more 
familiar unit.

> I ran a short simulation with pull_coord1_rate = 0, and when I did that I
> got reasonable forces such as 40-60 kj/mol/nm (??) but still not a zero
> force at time t=0. Please let me know if this is normal behavior or not.

Sorry, can't tell without fully analyzing all of your files (not something I 
have time for).  Check what grompp reports as the reference distance at t=0 vs. 
what you calculate in the input coordinate file/first frame of the trajectory. 
I've never used the cylinder geometry; could be something specific to that.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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