[gmx-users] gmx distance

[Justin Lemkul]

On 6/10/15 3:58 AM, Ming Tang wrote:
> 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

No, this is not right.  The spring is attached to both groups, but then extends 
along the vector between the two groups with a predictable displacement.  The 
force on the spring is then interpolated onto the pulled group, which will 
eventually lead to a displacement.

> 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

This just means your axis convention is likely backwards from what you think it is.

-Justin

> 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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-- 
==================================================

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

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