ana johari wrote:
Dear user,
Tanks for your attention ,I read about trjconv,but I want to know is it
necessary to back to the exact fram befor molecule split happens and
then center the molecule by trjconv command?
If the protein starts in the center of the box, just use trjconv in conjunction
with your original .tpr file. A suggested trjconv workflow is on the page
Tsjerk pointed you to.
The other point,if you attention to my value”edit conf d=0.9 and during
MD rvdw=1..4” is it broke the rule of periodic boundary condition or not?
In principle, no, as long as your box does not significantly deform. Check with
g_mindist -pi.
-Justin
tanks
------------------------------------------------------------------------
*From:* Tsjerk Wassenaar <tsje...@gmail.com>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Fri, April 1, 2011 1:29:19 PM
*Subject:* Re: [gmx-users] FW: protein split over boundary
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-TAW
On Fri, Apr 1, 2011 at 10:53 AM, anahita <ana_j0...@yahoo.com
<mailto:ana_j0...@yahoo.com>> wrote:
>
>
>
>
> From: anahita [mailto:ana_j0...@yahoo.com <mailto:ana_j0...@yahoo.com>]
> Sent: Friday, April 01, 2011 1:13 PM
> To: 'gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>'
> Subject: protein split over boundary
>
>
>
> Dear user,
>
> Hello, I appreciate if somebody help me. During the simulation of my
protein
> I didn’t get any error but after 1ns of MD
>
> my molecule was split over boundary in cubic box. it means some part
of it
> enter the other side of the box.
>
> At first,For decreasing the cost of simulation, in “editconf” command
I set
> the number “d” on 0.9 to decease the box size. I want to mention that
> during the calculation my rvdw is 1.4.
>
> I want to know instead of problem of visualization, the other things is
> fine?
>
> Best regards.
>
> A. johari
>
> --
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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--
========================================
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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