[gmx-users] smooth trajectory

[Justin A. Lemkul]

ana johari wrote:
> dear Justin,
> 
> tanks for your kindness.I would like to follow up what you say,but I 
> want to have simulation without wraping.
> could these command be helpful?

No.  A modified trajectory should not be used for further simulation.  "Fixing" 
periodicity is only useful for visualization and, in some cases, proper 
analysis.  All simulations should be conducted from unmodified files.

-Justin

> trjconv -s first1ns.tpr -f whatever_trajectory_you_want(xtc after 3ns 
> simulation).xtc -pbc mol -center -o fit.gro
>  grompp -f md300.mdp -c fit.gro -p n.top -o md300.tpr -n n.ndx
>  nohup mpirun -np 8 mdrun -s md300.tpr  -o md300.trr -c md300.gro -g 
> md300.log -e md300.edr&
> best regards
> 
> 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 <mailto:jalemkul at vt.edu>>
>  > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto: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> <mailto: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> <mailto: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>> <mailto: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>> <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 
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>  >  >  > 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/> <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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-- 
========================================

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

========================================