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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin Lemkul [jalem...@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
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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Baltimore, MD 21201
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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