[gmx-users] FW: protein split over boundary
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 1 13:34:27 CEST 2011
ana johari wrote:
> dear user,
>
> Tanks for your advice,
>
> But the mdrun is know on the step of 33562880 but the protein was split
> at the first 1ns of MD. is <http://md.is/> it necessary to use “tpbconv”
> command and extract the *.tpr file just after first 1 ns and then use
> trjconv –ur compact as command.
>
No. If the starting configuration had the protein properly centered in the box,
then a simple:
trjconv -s first.tpr -f whatever_trajectory_you_want.xtc -pbc mol -center
should work to make molecules whole and center the protein in the box.
-Justin
> Best regards,
>
>
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Fri, April 1, 2011 2:52:53 PM
> *Subject:* Re: [gmx-users] FW: protein split over boundary
>
>
>
> 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 <tsjerkw at gmail.com <mailto:tsjerkw at gmail.com>>
> > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at 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_j0000 at yahoo.com
> <mailto:ana_j0000 at yahoo.com> <mailto:ana_j0000 at yahoo.com
> <mailto:ana_j0000 at yahoo.com>>> wrote:
> > >
> > >
> > >
> > >
> > > From: anahita [mailto:ana_j0000 at yahoo.com
> <mailto:ana_j0000 at yahoo.com> <mailto:ana_j0000 at yahoo.com
> <mailto:ana_j0000 at yahoo.com>>]
> > > Sent: Friday, April 01, 2011 1:13 PM
> > > To: 'gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at 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 <http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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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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