@Xavier:<br>So, this means:<br><br>nstxtcout from 10 to 1<br>nsteps from 100000 to 10000<br>nstlog from 10 to 1<br>nstenergy from 10 to 1<br>nstlist from 5 to 1.<br><br>This is what should be changed in the .mdp file in order to get a proper rerun g_energy analysis?
<br><br>@Berk: Thanks a lot for the clarification. But still could not understand why there is any need for using g_analyze. Could you ple clarify this point out for me?<br><br>Thanks a lot for everybody in advance!<br><br>
Jones<br><br><div><span class="gmail_quote">On 8/6/07, <b class="gmail_sendername">Xavier Periole</b> <<a href="mailto:X.Periole@rug.nl">X.Periole@rug.nl</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>You should also update your neighbor list every step (10ps). if you<br>the original 5/10 steps frequency mdrun -rerun will update them every<br>5/10*10ps ...<br><br>XAvier<br><br>>>From: "Jones de Andrade" <
<a href="mailto:johannesrs@gmail.com">johannesrs@gmail.com</a>><br>>>Reply-To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>>To: "Discussion list for GROMACS users" <
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>>Subject: Re: [gmx-users] how to remove an energy contribution in gromacs?<br>>>Date: Mon, 6 Aug 2007 11:13:44 -0300<br>>><br>>>Hi both.
<br>>><br>>>@ Mark: thanks mark. Have to admit that I haven't thought about the<br>>>exclusions possibility. Specially because I was looking for a simple way of<br>>>doing it without removing the dynamics related to these forces from the
<br>>>simulation itself. So, changing the nexcl looked a bit easier to do.<br>>><br>>>@ Berk:<br>>><br>>> > This seems the right approach to me.<br>>> ><br>>> > I don't know what you are doing exactly.
<br>>> > But are you aware that the averages in g_energy and in the log file<br>>> > are using every integration step, whereas with rerun you only get values<br>>> > for every frame in your trajectory?
<br>>> > I think the averages of mdrun -rerun are still incorrect, you need to<br>>>use<br>>> > the average of the values in the energy.xvg file.<br>>><br>>><br>>> Ok, let me see if I understood: This means that, if I simulated
<br>>>originally<br>>>with the .mdp saying for the system to save the trajectory every 10 time<br>>>steps, and even with this fact still mentioned in the .mdp file for the<br>>>"mdrun -rerun" job, it would barelly mean that the energies would be divided
<br>>>by a factor of 10, and the "oscilations" are due to the reduction in the<br>>>statistics? Is it correct?<br>><br>> Yes.<br>> The factor will not be exactly 10 though, since there are some end effects.
<br>> With may frames it will be very close to 10 though.<br>><br>>><br>>>So, the proper way of doing if is not just keep on saying on the .mdp file<br>>>that it's saved every 10 time steps, but rather more or I just get the
<br>>>results and multiply them by 10, or make the rerun informing a 10 times<br>>>larger time-step?<br>><br>> You can not fix the problems caused by this "bug".<br>>For the average values of the rerun you should just run g_energy
<br>> and extract the average from the energy.xvg file using for instance<br>>g_analyze.<br>><br>> Berk.<br>><br>> _________________________________________________________________<br>> Hotmail en Messenger on the move
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<a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br>-----------------------------------------------------<br>XAvier Periole - PhD<br><br>1- Institute of Molecular Assemblies
<br> City University of New York - USA<br>2- Molecular Dynamics-Group<br> University of Groningen - The Netherlands<br><a href="http://md.chem.rug.nl/~periole">http://md.chem.rug.nl/~periole</a><br>-----------------------------------------------------
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