[gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)
Shilpi Chaurasia
shilpi.chaurasia at unimi.it
Tue Sep 13 15:24:27 CEST 2011
Dear Justin,
Thanks a lot for your reply.
Here I am providing the data and explaining the problem in detail:
I hope that it will help you in understanding in a better way.
Considering the tetramer as 'abcd'. 'ab' as one dimer and 'cd' as
another, I want to separate 'ab' and 'cd'. Length of each dimer is 8 nm,
so the tetramer (initial configuration) is approximately 16 nm and I
have used a cubic box of 30 nm. Two groups (reference group and pull
group) are decided on the basis of residue numbers forming 'ab' as
reference grp and 'bc' as pull group by making an index file.
I have verified that the initial configuration does not split across
periodic boundaries, it is always inside the box throughout the
simulation. Moreover, the initial distance is not equal to box vector.
By g_dist , I have tried to calculate the distance between the two groups and it came out to be approx. 15 nm (Please have a look at the dist.xvg
file at the end). Do you think that in the first ps time frame, should
it get separated by 15 nm?? Please correct me if I have done anything
wrong.
By mistake, in my last mail I wrote that I need to pull along Y axis. In
actual, it is Z-axis and I have used pull_dim N N Y. So it is just the
mistake in writing the mail.
Please let me know do you need any other data or parameters that I have used during this simulation.
An early reply would me much appreciated.
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dist.xvg
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# This file was created Tue Sep 13 11:09:23 2011
# by the following command:
# g_dist -f tub_pull.xtc -s tub_pull.tpr -n index.ndx
#
# g_dist is part of G R O M A C S:
#
# Giving Russians Opium May Alter Current Situation
#
@ title "Distance"
@ xaxis label "Time (ps)"
@ yaxis label "Distance (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 "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
0.0000000 15.0342455 -0.7714367 -0.9718266 14.9829559
0.5000000 15.0345469 -0.7726345 -0.9766102 -14.9828863
1.0000000 15.0345631 -0.7665710 -0.9862967 -14.9825792
1.5000000 15.0343399 -0.7575226 -0.9916229 14.9824638
2.0000000 15.0335970 -0.7490749 -0.9957008 -14.9818726
2.5000000 15.0322971 -0.7446661 -0.9996347 -14.9805260
3.0000000 15.0341187 -0.7364883 -1.0029345 -14.9825373
3.5000000 15.0331717 -0.7328205 -1.0078001 14.9814405
4.0000000 15.0311899 -0.7334194 -1.0118599 14.9791489
4.5000000 15.0334759 -0.7351160 -1.0128736 14.9812908
5.0000000 15.0336533 -0.7327585 -1.0102243 14.9817638
5.5000000 15.0327044 -0.7342167 -1.0076447 14.9809132
6.0000000 15.0335188 -0.7365904 -1.0090990 -14.9815168
6.5000000 15.0296631 -0.7375288 -1.0111809 -14.9774609
7.0000000 15.0294476 -0.7318525 -1.0155020 -14.9772310
7.5000000 15.0322533 -0.7323456 -1.0173597 -14.9798965
8.0000000 15.0353861 -0.7333517 -1.0172930 14.9829950
8.5000000 15.0323915 -0.7285290 -1.0122719 14.9805660
9.0000000 15.0284719 -0.7241497 -1.0072327 14.9771843
9.5000000 15.0285101 -0.7232113 -1.0051012 14.9774113
10.0000000 15.0306396 -0.7257242 -1.0020084 14.9796333
10.5000000 15.0324621 -0.7242069 -0.9959688 14.9819384
11.0000000 15.0324860 -0.7183657 -0.9881392 -14.9827623
11.5000000 15.0308609 -0.7121477 -0.9848318 -14.9816465
12.0000000 15.0318832 -0.7091122 -0.9842033 14.9828577
12.5000000 15.0316772 -0.7063818 -0.9834919 -14.9828262
13.0000000 15.0291939 -0.7024584 -0.9846754 -14.9804420
13.5000000 15.0307999 -0.7052488 -0.9864941 14.9818020
14.0000000 15.0286407 -0.7049980 -0.9902172 14.9794016
14.5000000 15.0301456 -0.7010813 -0.9916439 -14.9810019
15.0000000 15.0305882 -0.6967783 -0.9922857 -14.9816036
15.5000000 15.0319242 -0.6941795 -0.9950562 14.9828815
16.0000000 15.0315027 -0.6892128 -0.9928131 14.9828358
16.5000000 15.0314274 -0.6889334 -0.9883585 -14.9830685
17.0000000 15.0296593 -0.6906672 -0.9852924 14.9814167
17.5000000 15.0277662 -0.6964712 -0.9844646 -14.9793034
18.0000000 15.0301647 -0.7006731 -0.9863977 -14.9813862
18.5000000 15.0285692 -0.7027130 -0.9882107 14.9795704
19.0000000 15.0304384 -0.7040758 -0.9874868 -14.9814291
19.5000000 15.0310335 -0.7008915 -0.9824295 -14.9825077
20.0000000 15.0304193 -0.6977320 -0.9794283 14.9822359
20.5000000 15.0306473 -0.6955061 -0.9762669 14.9827747
21.0000000 15.0293531 -0.6917162 -0.9746027 14.9817610
21.5000000 15.0295181 -0.6870613 -0.9746943 -14.9821339
22.0000000 15.0302134 -0.6855507 -0.9771519 14.9827404
22.5000000 15.0306492 -0.6869965 -0.9785366 14.9830208
23.0000000 15.0285063 -0.6840801 -0.9742985 -14.9812803
23.5000000 15.0265427 -0.6824503 -0.9738894 14.9794121
24.0000000 15.0262260 -0.6803436 -0.9716139 14.9793377
24.5000000 15.0266447 -0.6778135 -0.9723339 -14.9798260
25.0000000 15.0236931 -0.6710443 -0.9711208 -14.9772491
Best regards,
Shilpi Chaurasia
On 09/09/11, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
>
>
> Shilpi Chaurasia wrote:
> > I am trying to pull apart two dimers of tubulin protein joined together, to form two separate dimers by steered molecular dynamics using Pull code. The objective is to separate the dimers by pulling along one axis only (Y axis). I ran the simulation for 25 ps and it accomplished well but while visualizing the trajectory in VMD, in the very beginning (first frame), dimers are at distance which is much greater than expected. I expected that in first frame they should not have separated too much (i.e. in just 1 ps, they are at greater distance) I guess this is unusual. Please let me know where I am doing wrong? I have used the following pull code:
> >
>
> Actual numbers would help. Is your initial configuration simply split across periodic boundaries? If the initial distance is roughly equivalent to one of the box vectors, then that's the case. Otherwise, please provide real data and check to make sure your pull groups are what you think they are.
>
> >pull = umbrella
> >pull_geometry = distance
> >pull_dim = N N Y
>
> Note that you're not actually pulling along Y as you state above. Here, you're pulling along Z. Perhaps that's one issue.
>
> -Justin
>
> >pull_start = yes pull_init1 = 0.0
> >pull_ngroups = 1
> >pull_group0 = dimer_ref ; reference group (based on index file)
> >pull_group1 = dimer_pull ; pull group
> >pull_rate1 = 0.1 pull_k1 = 1000 pull_nstfout = 10 pull_nstxout = 10
> >
> >best regards,
> >Shilpi Chaurasia
> >
>
> --
> ========================================
>
> 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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