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On 16/02/2011 10:30 PM, ifat shub wrote:
<blockquote
cite="mid:AANLkTi=71Moj0kH4=TR3_gDh54b1WsnEi0HUNDx++MQq@mail.gmail.com"
type="cite">
<div dir="ltr">
<div><br>
Hi Tsjerk,</div>
<div>Thank you for your reply.</div>
<div>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?</div>
</div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<br>
<blockquote
cite="mid:AANLkTi=71Moj0kH4=TR3_gDh54b1WsnEi0HUNDx++MQq@mail.gmail.com"
type="cite">
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<div class="gmail_quote">
<blockquote style="border-left: 1px solid rgb(204, 204, 204);
margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
class="gmail_quote">message: 4<br>
Date: Wed, 16 Feb 2011 11:19:14 +0200<br>
From: ifat shub <<a moz-do-not-send="true"
href="mailto:shubifat@gmail.com">shubifat@gmail.com</a>><br>
Subject: [gmx-users] Periodic Boundary Conditions g_mindist
-pi<br>
To: <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<AANLkTi=<a moz-do-not-send="true"
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<br>
Hi,<br>
<br>
<br>
<br>
I am running a simulation on the complex 1aik.pdb in 310K. I
wanted to see<br>
if the complex is seeing its next periodic image, so I used
the g_mindist<br>
command with the -pi option. My command line was:<br>
<br>
g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi<br>
<br>
The output (see below) was stable until ~344ps when there is
a jump in the<br>
max internal distance (third column) from ~6nm to ~22nm.
After the jump the<br>
numbers are reduced back to ~6nm and remained stable until
the run is<br>
completed at 1ns.<br>
<br>
Does anyone know how to explain this jump? Is this a real
problem or just a<br>
visualization artifact? Is there a way to avoid such jumps?<br>
<br>
<br>
<br>
Here is the mdp file I used:<br>
<br>
------run.mdp------<br>
<br>
integrator = md<br>
<br>
nsteps = 1000000<br>
<br>
dt = 0.001<br>
<br>
coulombtype = pme<br>
<br>
vdw-type = cut-off<br>
<br>
tcoupl = Berendsen<br>
<br>
tc-grps = protein non-protein<br>
<br>
tau-t = 0.1 0.1<br>
<br>
ref-t = 310 310<br>
<br>
nstxout = 100<br>
<br>
nstvout = 0<br>
<br>
nstxtcout = 100<br>
<br>
nstenergy = 100<br>
<br>
comm_mode = Linear ; Angular<br>
<br>
comm_grps = Protein<br>
<br>
xtc_grps = Protein<br>
<br>
energygrps = Protein<br>
<br>
------------------<br>
<br>
<br>
<br>
Thanks,<br>
<br>
Ifat<br>
<br>
<br>
<br>
The output:<br>
<br>
343.7 10.813 5.924 16.445 16.445 16.445<br>
<br>
343.8 10.809 5.949 16.445 16.445 16.445<br>
<br>
343.9 10.804 5.959 16.445 16.445 16.445<br>
<br>
344 10.808 5.974 16.445 16.445 16.445<br>
<br>
344.1 0.18 21.982 16.445 16.445 16.445<br>
<br>
344.2 10.778 5.977 16.445 16.445 16.445<br>
<br>
344.3 10.768 5.996 16.445 16.445 16.445<br>
<br>
344.4 10.764 6.016 16.445 16.445 16.445<br>
<br>
344.5 10.722 6.029 16.445 16.445 16.445<br>
<br>
344.6 10.774 6.01 16.445 16.445 16.445<br>
<br>
344.7 0.174 21.984 16.445 16.445 16.445<br>
<br>
344.8 0.176 21.98 16.445 16.445 16.445<br>
<br>
344.9 0.17 22.002 16.445 16.445 16.445<br>
<br>
345 0.173 21.981 16.445 16.445 16.445<br>
<br>
345.1 0.191 21.954 16.445 16.445 16.445<br>
<br>
345.2 0.183 21.958 16.445 16.445 16.445<br>
<br>
345.3 0.181 22.012 16.445 16.445 16.445<br>
<br>
345.4 0.17 22.054 16.445 16.445 16.445<br>
<br>
345.5 0.168 22.054 16.445 16.445 16.445<br>
<br>
345.6 0.189 22.039 16.445 16.445 16.445<br>
<br>
345.7 0.171 22.007 16.445 16.445 16.445<br>
<br>
345.8 0.186 22.031 16.445 16.445 16.445<br>
<br>
345.9 0.171 22.077 16.445 16.445 16.445<br>
<br>
346 0.187 21.99 16.445 16.445 16.445<br>
<br>
346.1 0.173 21.984 16.445 16.445 16.445<br>
<br>
346.2 0.181 22.02 16.445 16.445 16.445<br>
<br>
346.3 10.82 5.984 16.445 16.445 16.445<br>
<br>
346.4 10.81 6.002 16.445 16.445 16.445<br>
<br>
346.5 10.819 6.008 16.445 16.445 16.445<br>
<br>
346.6 10.813 5.996 16.445 16.445 16.445<br>
<br>
346.7 10.781 6.006 16.445 16.445 16.445<br>
<br>
346.8 10.793 6.026 16.445 16.445 16.445<br>
<br>
346.9 10.745 5.985 16.445 16.445 16.445<br>
<br>
347 10.762 5.999 16.445 16.445 16.445<br>
<br>
347.1 10.781 5.984 16.445 16.445 16.445<br>
<br>
347.2 10.784 6.002 16.445 16.445 16.445<br>
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------------------------------<br>
<br>
Message: 5<br>
Date: Wed, 16 Feb 2011 10:43:56 +0100<br>
From: Tsjerk Wassenaar <<a moz-do-not-send="true"
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
Subject: Re: [gmx-users] Periodic Boundary Conditions
g_mindist -pi<br>
To: Discussion list for GROMACS users <<a
moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
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Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Hi Ifat,<br>
<br>
I guess this is a jump over the periodic boundaries. You
should remove<br>
jumps from the trajectory (-pbc nojump) before running
g_mindist -pi.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
On Wed, Feb 16, 2011 at 10:19 AM, ifat shub <<a
moz-do-not-send="true" href="mailto:shubifat@gmail.com">shubifat@gmail.com</a>>
wrote:<br>
> Hi,<br>
><br>
><br>
><br>
> I am running a simulation on the complex 1aik.pdb in
310K. I wanted to see<br>
> if the complex is seeing its next periodic image, so I
used the g_mindist<br>
> command with the -pi option. My command line was:<br>
><br>
> g_mindist -f run.xtc -s run.gro -n index.ndx -od
tmp.xvg -pi<br>
><br>
> The output (see below) was stable until ~344ps when
there is a jump in the<br>
> max internal distance (third column) from ~6nm to
~22nm. After the jump the<br>
> numbers are reduced back to ~6nm and remained stable
until the run is<br>
> completed at 1ns.<br>
><br>
> Does anyone know how to explain this jump? Is this a
real problem or just a<br>
> visualization artifact? Is there a way to avoid such
jumps?<br>
><br>
><br>
><br>
> Here is the mdp file I used:<br>
><br>
> ------run.mdp------<br>
><br>
> integrator = md<br>
><br>
> nsteps = 1000000<br>
><br>
> dt = 0.001<br>
><br>
> coulombtype = pme<br>
><br>
> vdw-type = cut-off<br>
><br>
> tcoupl = Berendsen<br>
><br>
> tc-grps = protein non-protein<br>
><br>
> tau-t = 0.1 0.1<br>
><br>
> ref-t = 310 310<br>
><br>
> nstxout = 100<br>
><br>
> nstvout = 0<br>
><br>
> nstxtcout = 100<br>
><br>
> nstenergy = 100<br>
><br>
> comm_mode = Linear ; Angular<br>
><br>
> comm_grps = Protein<br>
><br>
> xtc_grps = Protein<br>
><br>
> energygrps = Protein<br>
><br>
> ------------------<br>
><br>
><br>
><br>
> Thanks,<br>
><br>
> Ifat<br>
><br>
><br>
><br>
> The output:<br>
><br>
> 343.7 10.813 5.924 16.445 16.445 16.445<br>
><br>
> 343.8 10.809 5.949 16.445 16.445 16.445<br>
><br>
> 343.9 10.804 5.959 16.445 16.445 16.445<br>
><br>
> 344 10.808 5.974 16.445 16.445 16.445<br>
><br>
> 344.1 0.18 21.982 16.445 16.445 16.445<br>
><br>
> 344.2 10.778 5.977 16.445 16.445 16.445<br>
><br>
> 344.3 10.768 5.996 16.445 16.445 16.445<br>
><br>
> 344.4 10.764 6.016 16.445 16.445 16.445<br>
><br>
> 344.5 10.722 6.029 16.445 16.445 16.445<br>
><br>
> 344.6 10.774 6.01 16.445 16.445 16.445<br>
><br>
> 344.7 0.174 21.984 16.445 16.445 16.445<br>
><br>
> 344.8 0.176 21.98 16.445 16.445 16.445<br>
><br>
> 344.9 0.17 22.002 16.445 16.445 16.445<br>
><br>
> 345 0.173 21.981 16.445 16.445 16.445<br>
><br>
> 345.1 0.191 21.954 16.445 16.445 16.445<br>
><br>
> 345.2 0.183 21.958 16.445 16.445 16.445<br>
><br>
> 345.3 0.181 22.012 16.445 16.445 16.445<br>
><br>
> 345.4 0.17 22.054 16.445 16.445 16.445<br>
><br>
> 345.5 0.168 22.054 16.445 16.445 16.445<br>
><br>
> 345.6 0.189 22.039 16.445 16.445 16.445<br>
><br>
> 345.7 0.171 22.007 16.445 16.445 16.445<br>
><br>
> 345.8 0.186 22.031 16.445 16.445 16.445<br>
><br>
> 345.9 0.171 22.077 16.445 16.445 16.445<br>
><br>
> 346 0.187 21.99 16.445 16.445 16.445<br>
><br>
> 346.1 0.173 21.984 16.445 16.445 16.445<br>
><br>
> 346.2 0.181 22.02 16.445 16.445 16.445<br>
><br>
> 346.3 10.82 5.984 16.445 16.445 16.445<br>
><br>
> 346.4 10.81 6.002 16.445 16.445 16.445<br>
><br>
> 346.5 10.819 6.008 16.445 16.445 16.445<br>
><br>
> 346.6 10.813 5.996 16.445 16.445 16.445<br>
><br>
> 346.7 10.781 6.006 16.445 16.445 16.445<br>
><br>
> 346.8 10.793 6.026 16.445 16.445 16.445<br>
><br>
> 346.9 10.745 5.985 16.445 16.445 16.445<br>
><br>
> 347 10.762 5.999 16.445 16.445 16.445<br>
><br>
> 347.1 10.781 5.984 16.445 16.445 16.445<br>
><br>
> 347.2 10.784 6.002 16.445 16.445 16.445<br>
><br>
><br>
><br>
><br>
><br>
> --<br>
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href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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Use the<br>
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><br>
<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and
Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<br>
<br>
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