[gmx-users] smooth trajectory

ana johari ana_j0000 at yahoo.com
Sat Apr 2 21:23:50 CEST 2011 

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?
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>
> *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
>  >  >
>  >  > --
>  >  > gmx-users mailing list    gmx-users at gromacs.org 
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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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