[gmx-users] gmx distance

[Ming Tang]

Dear Justin,

Thank you so much. My first understanding was that the spring is connected with both ends of the protein and its original length is identical to the length of protein.  According to your explanation, the distance of COM between both ends of the protein should remain to be 0 until the pulling force of the spring overcomes the restoring force. Am I right? But the curve from pullx.xvg shows an increase from -4.5nm and the curve from dist.xvg undergoes a decrease from 4.5nm o 0.5nm at the beginning. If my understanding of your explanation is correct, then there is something wrong with my simulation. But the configuration is right and the trend of the pulling force is correct as well. Can you give me some guidance?

I will learn python. Thanks.

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Tuesday, 9 June 2015 9:41 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] gmx distance



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

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

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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