On 6/6/13 5:17 AM, Bastien Loubet wrote:
I update the post to say that we tried to make a rerun of the trajectory on
our local machine and the output of the pullx.xvg file (created with the
option -px of mdrun) is:
************************************************
# This file was created Wed Jun 5 12:15:49 2013
# by the following command:
# mdrun -s ../conf10.tpr -rerun ../conf10.xtc -px pullx_conf10.xvg -pf
pullf_conf10.xvg -nt 6 -v
#
# mdrun is part of G R O M A C S:
#
# Gravel Rubs Often Many Awfully Cauterized Sores
#
@ 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 X"
@ s1 legend "0 Y"
@ s2 legend "0 Z"
@ s3 legend "1 dX"
@ s4 legend "1 dY"
@ s5 legend "1 dZ"
0.0000 3.47835 5.10501 11.644 -0.378345 1.13499 1.73604
20.0000 3.47852 5.12016 11.6554 -0.446518 1.07184 1.69255
40.0000 3.49803 5.12013 11.6612 -0.350032 1.12387 1.75475
(...)
**********************************************
The output of the pullx.xvg file is indeed the distance between the two pull
groups, but this is very different numbers than the one obtained during the
simulation on a cluster (see above post).
So the question stand what are the numbers given in the pullx.xvg file
created during the original simulation ?
http://lists.gromacs.org/pipermail/gmx-users/2009-June/042887.html
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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