[gmx-users] Re: Periodic Boundary Conditions g_mindist -pi
ifat shub
shubifat at gmail.com
Wed Feb 16 12:30:29 CET 2011
Hi Tsjerk,
Thank you for your reply.
I am aware of the trajconv option but I wanted to know if there is a way to
avoid these kind of jumps over the periodic boundaries during the mdrun and
not post process?
Thanks,
Ifat
message: 4
> Date: Wed, 16 Feb 2011 11:19:14 +0200
> From: ifat shub <shubifat at gmail.com>
> Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi
> To: gmx-users at gromacs.org
> Message-ID:
> <AANLkTi=sgjfTmrf-0nVmZZOgfs+xhyxv5u6GGFNHR6hp at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
>
>
> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see
> if the complex is seeing its next periodic image, so I used the g_mindist
> command with the -pi option. My command line was:
>
> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>
> The output (see below) was stable until ~344ps when there is a jump in the
> max internal distance (third column) from ~6nm to ~22nm. After the jump the
> numbers are reduced back to ~6nm and remained stable until the run is
> completed at 1ns.
>
> Does anyone know how to explain this jump? Is this a real problem or just a
> visualization artifact? Is there a way to avoid such jumps?
>
>
>
> Here is the mdp file I used:
>
> ------run.mdp------
>
> integrator = md
>
> nsteps = 1000000
>
> dt = 0.001
>
> coulombtype = pme
>
> vdw-type = cut-off
>
> tcoupl = Berendsen
>
> tc-grps = protein non-protein
>
> tau-t = 0.1 0.1
>
> ref-t = 310 310
>
> nstxout = 100
>
> nstvout = 0
>
> nstxtcout = 100
>
> nstenergy = 100
>
> comm_mode = Linear ; Angular
>
> comm_grps = Protein
>
> xtc_grps = Protein
>
> energygrps = Protein
>
> ------------------
>
>
>
> Thanks,
>
> Ifat
>
>
>
> The output:
>
> 343.7 10.813 5.924 16.445 16.445 16.445
>
> 343.8 10.809 5.949 16.445 16.445 16.445
>
> 343.9 10.804 5.959 16.445 16.445 16.445
>
> 344 10.808 5.974 16.445 16.445 16.445
>
> 344.1 0.18 21.982 16.445 16.445 16.445
>
> 344.2 10.778 5.977 16.445 16.445 16.445
>
> 344.3 10.768 5.996 16.445 16.445 16.445
>
> 344.4 10.764 6.016 16.445 16.445 16.445
>
> 344.5 10.722 6.029 16.445 16.445 16.445
>
> 344.6 10.774 6.01 16.445 16.445 16.445
>
> 344.7 0.174 21.984 16.445 16.445 16.445
>
> 344.8 0.176 21.98 16.445 16.445 16.445
>
> 344.9 0.17 22.002 16.445 16.445 16.445
>
> 345 0.173 21.981 16.445 16.445 16.445
>
> 345.1 0.191 21.954 16.445 16.445 16.445
>
> 345.2 0.183 21.958 16.445 16.445 16.445
>
> 345.3 0.181 22.012 16.445 16.445 16.445
>
> 345.4 0.17 22.054 16.445 16.445 16.445
>
> 345.5 0.168 22.054 16.445 16.445 16.445
>
> 345.6 0.189 22.039 16.445 16.445 16.445
>
> 345.7 0.171 22.007 16.445 16.445 16.445
>
> 345.8 0.186 22.031 16.445 16.445 16.445
>
> 345.9 0.171 22.077 16.445 16.445 16.445
>
> 346 0.187 21.99 16.445 16.445 16.445
>
> 346.1 0.173 21.984 16.445 16.445 16.445
>
> 346.2 0.181 22.02 16.445 16.445 16.445
>
> 346.3 10.82 5.984 16.445 16.445 16.445
>
> 346.4 10.81 6.002 16.445 16.445 16.445
>
> 346.5 10.819 6.008 16.445 16.445 16.445
>
> 346.6 10.813 5.996 16.445 16.445 16.445
>
> 346.7 10.781 6.006 16.445 16.445 16.445
>
> 346.8 10.793 6.026 16.445 16.445 16.445
>
> 346.9 10.745 5.985 16.445 16.445 16.445
>
> 347 10.762 5.999 16.445 16.445 16.445
>
> 347.1 10.781 5.984 16.445 16.445 16.445
>
> 347.2 10.784 6.002 16.445 16.445 16.445
> -------------- next part --------------
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> ------------------------------
>
> Message: 5
> Date: Wed, 16 Feb 2011 10:43:56 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTinr05YyKV7rqzCSwEch=aBXFur+adKeNMxEMLEa at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Ifat,
>
> I guess this is a jump over the periodic boundaries. You should remove
> jumps from the trajectory (-pbc nojump) before running g_mindist -pi.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Feb 16, 2011 at 10:19 AM, ifat shub <shubifat at gmail.com> wrote:
> > Hi,
> >
> >
> >
> > I am running a simulation on the complex 1aik.pdb in 310K. I wanted to
> see
> > if the complex is seeing its next periodic image, so I used the g_mindist
> > command with the -pi option. My command line was:
> >
> > g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
> >
> > The output (see below) was stable until ~344ps when there is a jump in
> the
> > max internal distance (third column) from ~6nm to ~22nm. After the jump
> the
> > numbers are reduced back to ~6nm and remained stable until the run is
> > completed at 1ns.
> >
> > Does anyone know how to explain this jump? Is this a real problem or just
> a
> > visualization artifact? Is there a way to avoid such jumps?
> >
> >
> >
> > Here is the mdp file I used:
> >
> > ------run.mdp------
> >
> > integrator = md
> >
> > nsteps = 1000000
> >
> > dt = 0.001
> >
> > coulombtype = pme
> >
> > vdw-type = cut-off
> >
> > tcoupl = Berendsen
> >
> > tc-grps = protein non-protein
> >
> > tau-t = 0.1 0.1
> >
> > ref-t = 310 310
> >
> > nstxout = 100
> >
> > nstvout = 0
> >
> > nstxtcout = 100
> >
> > nstenergy = 100
> >
> > comm_mode = Linear ; Angular
> >
> > comm_grps = Protein
> >
> > xtc_grps = Protein
> >
> > energygrps = Protein
> >
> > ------------------
> >
> >
> >
> > Thanks,
> >
> > Ifat
> >
> >
> >
> > The output:
> >
> > 343.7 10.813 5.924 16.445 16.445 16.445
> >
> > 343.8 10.809 5.949 16.445 16.445 16.445
> >
> > 343.9 10.804 5.959 16.445 16.445 16.445
> >
> > 344 10.808 5.974 16.445 16.445 16.445
> >
> > 344.1 0.18 21.982 16.445 16.445 16.445
> >
> > 344.2 10.778 5.977 16.445 16.445 16.445
> >
> > 344.3 10.768 5.996 16.445 16.445 16.445
> >
> > 344.4 10.764 6.016 16.445 16.445 16.445
> >
> > 344.5 10.722 6.029 16.445 16.445 16.445
> >
> > 344.6 10.774 6.01 16.445 16.445 16.445
> >
> > 344.7 0.174 21.984 16.445 16.445 16.445
> >
> > 344.8 0.176 21.98 16.445 16.445 16.445
> >
> > 344.9 0.17 22.002 16.445 16.445 16.445
> >
> > 345 0.173 21.981 16.445 16.445 16.445
> >
> > 345.1 0.191 21.954 16.445 16.445 16.445
> >
> > 345.2 0.183 21.958 16.445 16.445 16.445
> >
> > 345.3 0.181 22.012 16.445 16.445 16.445
> >
> > 345.4 0.17 22.054 16.445 16.445 16.445
> >
> > 345.5 0.168 22.054 16.445 16.445 16.445
> >
> > 345.6 0.189 22.039 16.445 16.445 16.445
> >
> > 345.7 0.171 22.007 16.445 16.445 16.445
> >
> > 345.8 0.186 22.031 16.445 16.445 16.445
> >
> > 345.9 0.171 22.077 16.445 16.445 16.445
> >
> > 346 0.187 21.99 16.445 16.445 16.445
> >
> > 346.1 0.173 21.984 16.445 16.445 16.445
> >
> > 346.2 0.181 22.02 16.445 16.445 16.445
> >
> > 346.3 10.82 5.984 16.445 16.445 16.445
> >
> > 346.4 10.81 6.002 16.445 16.445 16.445
> >
> > 346.5 10.819 6.008 16.445 16.445 16.445
> >
> > 346.6 10.813 5.996 16.445 16.445 16.445
> >
> > 346.7 10.781 6.006 16.445 16.445 16.445
> >
> > 346.8 10.793 6.026 16.445 16.445 16.445
> >
> > 346.9 10.745 5.985 16.445 16.445 16.445
> >
> > 347 10.762 5.999 16.445 16.445 16.445
> >
> > 347.1 10.781 5.984 16.445 16.445 16.445
> >
> > 347.2 10.784 6.002 16.445 16.445 16.445
> >
> >
> >
> >
> >
> > --
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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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> End of gmx-users Digest, Vol 82, Issue 125
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