Wright, Louise wrote:
Hi
I am trying to use the pull code of gromacs (version 4.5.5) to constrain
the com of a number of groups (labelled CIT, CIT1, CIT2...) to a
reference group (labelled GOLD). This is the segment of the .mdp file I
have used:
;CoM pull calculations
pull = constraint
pull_geometry = distance
pull_dim = N N Y
pull_constr_tol = 1e-6
; add COM distance of starting config to pull_init
pull_start = yes
;frequency for writing COMS of all pull group
pull_nstxout = 10
;frequency for writing force of all pull group
pull_nstfout = 10
pull_ngroups = 12
;name of reference group
pull_group0 = GOLD
pull_group1 = CIT
pull_group2 = CIT1
pull_group3 = CIT2
pull_group4 = CIT3
pull_group5 = CIT4
pull_group6 = CIT5
pull_group7 = CIT6
pull_group8 = CIT7
pull_group9 = CIT8
pull_group10 = CIT9
pull_group11 = CIT10
pull_group12 = CIT11
;reference distance at t=0 (nm)
pull_rate1 = 0
pull_rate2 = 0
pull_rate3 = 0
pull_rate4 = 0
pull_rate5 = 0
pull_rate6 = 0
pull_rate7 = 0
pull_rate8 = 0
pull_rate9 = 0
pull_rate10 = 0
pull_rate11 = 0
pull_rate12 = 0
However, when I look at the output only the first pull group (CIT) is
being restrained at a constant com height from GOLD. The others move away.
output from pullx.xvg:
0.0400 0.717773 0.984186 0.977682 0.979256
0.975962 0.978739 0.974255 0.969942 0.97706
0.987668 1.00157 0.979894 0.982414
0.0500 0.717776 0.985442 0.977141 0.979625
0.976002 0.978158 0.973563 0.968578 0.97746
0.989067 1.00363 0.980026 0.983273
0.0600 0.717776 0.986709 0.976605 0.980068
0.976034 0.977671 0.973037 0.967893
0.977855 0.990371 1.00531 0.980148 0.984034
0.0700 0.717776 0.987965 0.976222 0.98048
0.976129 0.977231 0.972626 0.967535
0.978239 0.991569 1.00703 0.980298 0.984731
0.0800 0.717776 0.989129 0.976023 0.980946
0.976285 0.976717 0.972257 0.967184
0.978667 0.99272 1.0089 0.980504 0.985445
0.0900 0.717776 0.990186 0.97597 0.98157 0.976445
0.976252 0.971888 0.966841 0.97909 0.993944
1.01091 0.980784 0.986181
0.1000 0.717776 0.991179 0.976024 0.982275
0.9766 0.975847 0.971445 0.966549 0.979437
0.995328 1.01311 0.98115 0.986935
0.1100 0.717776 0.992167 0.976165 0.982984
0.976787 0.975344 0.970858 0.966275
0.979715 0.996957 1.01556 0.981619 0.987732
I was wondering what I have done wrong in the input .mdp file. >From
looking at the manual, I can't work it out since I think I have set it
up as shown.
Do the distances continually get larger? I see no clear evidence of that here,
but it is a short timeframe. The COM separation will fluctuate to a small
extent; you should not expect the distance to remain absolutely fixed.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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