[gmx-users] Re: Periodic Boundary Conditions g_mindist -pi
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Feb 16 13:54:53 CET 2011
On Wed, Feb 16, 2011 at 1:00 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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.
>
Or:
No. mdrun takes the internal representation that is most efficient,
and there are better things to do with expensive compute cluster time
than writing out a trajectory without jumps, which might not even be
what you want in the end. :)
Tsjerk
> Mark
>
>
>> 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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>
>
>
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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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