[gmx-users] gmx distance

[Ming Tang]

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 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? 

Thanks very much.

-----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: Sunday, 7 June 2015 11:51 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] gmx distance



On 6/5/15 9:49 PM, Ming Tang wrote:
> Thanks, Justin
>
> Using -pbc or not gives the same curve. I tried to guess the curve give the deviation of the two end groups, but the curve drops from around 4nm to 1nm at the beginning. I am really confused about this.
>

Without seeing the plots and the index groups, there's nothing I can guess.

-Justin

> -----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: Saturday, 6 June 2015 2:56 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gmx distance
>
>
>
> On 6/5/15 7:07 AM, Ming Tang wrote:
>> Dear gromacs experts,
>>
>> I am stretching a triple helix along z direction by fixing one end 
>> and pull the other. The helix length changes from 35nm to 50nm during the MD simulation. However, after using gmx distance -n index.ndx -f traj.trr -s topol.tpr -select 'com of group start plus com of group end' -oav dist.xvg
>> to get the distance between the two end groups,   I found that the distance varies from 2nm to 15nm during the simulation.
>> I am quite confused about this, because the original length of the helix is around 35nm. The configuration looks correct....
>> Am I wrong when using gmx distance?
>>
>
> Probably -pbc is relevant here.
>
>    -[no]pbc        (yes)
>        Use periodic boundary conditions for distance calculation
>
> You're likely getting the inter-image distance rather than the one within the unit cell.
>
> -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

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