[gmx-users] Re: Periodic Boundary Conditions g_mindist -pi
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Feb 16 13:00:32 CET 2011
On 16/02/2011 10:30 PM, ifat shub wrote:
>
> 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?
No. mdrun does not know in advance what your visualization requirements
are, and frankly there are better things to do with expensive compute
cluster time. Post-processing a small number of frames elsewhere is much
better use of resources.
Mark
> message: 4
> Date: Wed, 16 Feb 2011 11:19:14 +0200
> From: ifat shub <shubifat at gmail.com <mailto:shubifat at gmail.com>>
> Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Message-ID:
> <AANLkTi=sgjfTmrf-0nVmZZOgfs+xhyxv5u6GGFNHR6hp at mail.gmail.com
> <mailto:sgjfTmrf-0nVmZZOgfs%2Bxhyxv5u6GGFNHR6hp 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
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> ------------------------------
>
> Message: 5
> Date: Wed, 16 Feb 2011 10:43:56 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com <mailto: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
> <mailto:gmx-users at gromacs.org>>
> Message-ID:
> <AANLkTinr05YyKV7rqzCSwEch=aBXFur+adKeNMxEMLEa at mail.gmail.com
> <mailto:aBXFur%2BadKeNMxEMLEa 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
> <mailto: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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