<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>Thanks,</div>
<div>Ifat<br><br></div>
<div class="gmail_quote">
<blockquote style="BORDER-LEFT: #ccc 1px solid; 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 href="mailto:shubifat@gmail.com">shubifat@gmail.com</a>><br>
Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID:<br> <AANLkTi=<a href="mailto:sgjfTmrf-0nVmZZOgfs%2Bxhyxv5u6GGFNHR6hp@mail.gmail.com">sgjfTmrf-0nVmZZOgfs+xhyxv5u6GGFNHR6hp@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br><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>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html</a><br>
<br>------------------------------<br><br>Message: 5<br>Date: Wed, 16 Feb 2011 10:43:56 +0100<br>From: Tsjerk Wassenaar <<a 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 href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <AANLkTinr05YyKV7rqzCSwEch=<a href="mailto:aBXFur%2BadKeNMxEMLEa@mail.gmail.com">aBXFur+adKeNMxEMLEa@mail.gmail.com</a>><br>
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 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>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><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>
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