[gmx-users] gmx distance

[Justin Lemkul]

On 6/9/15 4:08 AM, Ming Tang wrote:
> Dear Justin,
>
> I have invited you to share the dist.xvg, please help to have a look. I
> cannot understand why does the distance between two ends start at around
> -4nm. In distance.mdp, I set pull rate to be 0.001nm/ps. After pulling 30ns,
> the COM distance should increase 30nm. Am I right? But the length of the

No, this is not right.  This means that the displacement of the spring is 30 nm 
in that time.  It does *not* mean that the net displacement imposed on the 
pulled coordinates is also 30 nm.  There are restoring forces within the protein 
structure that resist the applied force.  The spring will continue to pull until 
the pulling force overcomes the restoring force and induces displacement in the 
protein.

> helix aslo shows only a 15nm increase (see len-ahx.xvg). Another thing is,
> why does the length of the helix jump from 5ns to 10ns?  I found that the
> pullf.xvg records the force for every step, making it too large to be
> processed by excel. Is there any method that I can use to extract the pull
> force with specific time interval like using gmx distance -dt to get
> distance?

Don't box yourself in by relying on such programs.  Pick up any simple scripting 
language (Perl, Python, etc) and learn to use it.  Your life will be much easier.

-Justin

-- 
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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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