[gmx-users] umbrella sampling using pull codes

[mjyang]

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? 

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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