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 <shubi...@gmail.com <mailto:shubi...@gmail.com>>
Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID:
<AANLkTi=sgjftmrf-0nvmzzogfs+xhyxv5u6ggfnhr...@mail.gmail.com
<mailto:sgjftmrf-0nvmzzogfs%2bxhyxv5u6ggfnhr...@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 --------------
An HTML attachment was scrubbed...
URL:
http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html
------------------------------
Message: 5
Date: Wed, 16 Feb 2011 10:43:56 +0100
From: Tsjerk Wassenaar <tsje...@gmail.com <mailto:tsje...@gmail.com>>
Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID:
<AANLkTinr05YyKV7rqzCSwEch=abxfur+adkenmxem...@mail.gmail.com
<mailto:abxfur%2badkenmxem...@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 <shubi...@gmail.com
<mailto:shubi...@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
>
>
>
>
>
> --
> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
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
------------------------------
--
gmx-users mailing list
gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
End of gmx-users Digest, Vol 82, Issue 125
******************************************
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
