[gmx-users] Re: Fwd: about the pulling

[Tom]

Thanks Justin!

On 10/17/11, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Tom wrote:
>> Justin
>>
>> you have good experience of pulling.
>>
>> If you have time, please help with this publling problem:
>> abrupt change in sign of 1dZ on output file: pullx.xvg. Thanks a lot!
>>
>
> I already commented:
>
> http://lists.gromacs.org/pipermail/gmx-users/2011-October/065226.html
>
>> i am pulling A object towards B along z-axis. But system
>> has pbc on x, y and z. Is it because of the pbc image of B
>> object that make grmx confused to report the sign.
>>
>
> Likely.  If your box is not greater than about 16.3 nm in Z, then you'll
> have
> this problem.
>
>> In my system, A should be on the top of B in z-axis, but i just noticed
>> that at the intial step: 1dZ has been negative already.
>> It seems the system use the PBC image (in z-axis) of the reference object
>> B
>>  to cacluate 1dZ, right?
>
> Sounds right.
>
> -Justin
>
>> --------------------------------------
>> @    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  0.77622 -8.13474
>> ------------------------------------
>>
>> Thanks a lot for the help!
>>
>> Tom
>>
>> ---------- Forwarded message ----------
>> From: Tom <dnaafm at gmail.com>
>> Date: Sun, 16 Oct 2011 23:02:09 +0800
>> Subject: about the pulling
>> To: gmx-users <gmx-users at gromacs.org>
>>
>> Dear Gromacs Users or Developers,
>>
>> I am using the pulling the COM of object A towards B using:
>> ---------------------------------
>> pull                     = umbrella
>> pull_geometry            = distance
>> pull_dim                 = N N Y
>> pull_start               = yes
>> pull_ngroups             = 1
>> pull_group0              = B
>> pull_group1              = A
>> pull_rate1               = -0.00005714
>> pull_k1                  = 5000
>> -------------------------------
>> On the output file of pullx.xvg,  the sign of dZ
>> has been changed from negative to posivitve
>> or vice vrsa in all sudden. What does it mean?
>>
>> The following is an example:
>>
>> @    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"
>>
>> ---------------------------------------------------
>> 173.7400        0.77622 8.14856
>> 173.7500        0.77622 8.14897
>> 173.7600        0.77622 8.14938
>> 173.7700        0.77622 8.14977
>> 173.7800        0.77622 -8.14987
>> 173.7900        0.77622 -8.14954
>> 173.8000        0.77622 -8.14924
>> 173.8100        0.77622 -8.14895
>> ------------------------------------
>>
>>
>> Thanks a lot for the information!
>>
>> Thanks,
>>
>> Tom
>>
>
> --
> ========================================
>
> 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
>
> ========================================
>