# [gmx-users] umbrella sampling using pull codes

Justin Lemkul jalemkul at vt.edu
Fri Sep 13 04:48:03 CEST 2013

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On 9/12/13 10:41 PM, mjyang wrote:
> Dear Justin,
>
>     What is the meaning of the "minus number" for the distance in the 3rd column? Does it mean that the moving group is at the minus direction wrt the reference group along Z?
>

Yes, since it is a vector quantity.  The positions should be very apparent from
simple visualization.

-Justin

> Many thanks.
>
> Mingjun
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin Lemkul [jalemkul at vt.edu]
> Sent: Friday, September 13, 2013 10:33 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] umbrella sampling using pull codes
>
> On 9/12/13 10:18 PM, mjyang wrote:
>> Dear Justin,
>>
>> Thanks for your reply. I checked the content in pullx.xvg file as follows:
>> --------------------------------------------------------
>> # GRowing Old MAkes el Chrono Sweat
>> #
>> @    title "Pull COM"
>> @    xaxis  label "Time (ps)"
>> @    yaxis  label "Position (nm)"
>> @TYPE xy
>> @ view 0.15, 0.15, 0.75, 0.85
>> @ legend on
>> @ legend box on
>> @ legend loctype view
>> @ legend 0.78, 0.8
>> @ legend length 2
>> @ s0 legend "0 Z"
>> @ s1 legend "1 dZ"
>> 0.0000  6.50285 -0.206062
>> 10.0000 7.66133 -2.6497
>> 20.0000 7.65877 -2.65375
>> 30.0000 7.65128 -2.6575
>> 40.0000 7.64102 -2.66939
>> --------------------------------------------------------------
>>
>> The numbers in 1st column is time. What is the meaning of the numbers in the 2nd and 3rd columns?
>>
>
> Z-position of the reference group, distance between the groups along Z.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
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--
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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

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