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I switched to v-rescale for the thermostat and things look normal! <br>Thanks for the help<br>Antonia<br><br><br>> Date: Wed, 1 Apr 2009 12:11:47 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] (no subject)<br>> <br>> <br>> <br>> Antonia V. wrote:<br>> > > 1. A description of your system<br>> > <br>> > I have a system of 250 5CB molecules (it is a liquid crystal) which <br>> > means 4750 atoms.<br>> > <br>> > > 2. Anything else that was printed to screen or the .log file (that's <br>> > where the<br>> > > real error message will appear)<br>> > <br>> > On the screen the message was<br>> > [compute-0-4:01361] *** Process received signal ***<br>> > [compute-0-4:01361] Signal: Segmentation fault (11)<br>> > [compute-0-4:01361] Signal code: Address not mapped (1)<br>> > [compute-0-4:01361] Failing at address: 0x1913c280<br>> > [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70]<br>> > [compute-0-4:01361] [ 1] mdrun [0x6a46cd]<br>> > [compute-0-4:01361] *** End of error message ***<br>> > Segmentation fault<br>> > <br>> > and the last thing that was written in the md.log file is<br>> > <br>> > Step Time Lambda<br>> > 0 0.00000 0.00000<br>> > <br>> > Grid: 8 x 8 x 8 cells<br>> > Energies (kJ/mol)<br>> > Bond Angle Proper Dih. LJ (SR) Coulomb (SR)<br>> > 3.12078e+03 7.44768e+04 5.19128e+03 -1.67708e+04 -1.07965e+03<br>> > Coul. recip. Potential Kinetic En. Total Energy Temperature<br>> > -6.75318e+03 5.81852e+04 2.02196e+01 5.82054e+04 3.41383e-01<br>> > Pressure (bar)<br>> > -2.55714e+03<br>> > <br>> <br>> Your potential energy has spiked to a very large value. That indicates you <br>> still have some bad contacts in the system.<br>> <br>> > > 3. What happened in the EM procedure?<br>> > After the EM (steep) the forces were minimized to the desired accuracy <br>> > (Tolerance (Fmax) = 1.00000e+02)<br>> > <br>> <br>> Was the potential reasonable? See above.<br>> <br>> > > 4. What .mdp parameters you are using<br>> > I use a time step of 2fs, PME for the electrostatics, a quite large <br>> > cut-off (1.2), the nose-hoover thermostat (340K)<br>> > <br>> <br>> Well, these are not all of your parameters, surely (it's best to post your whole <br>> .mdp file). If you are going for 340 K, you can see from your .log file that <br>> the temperature is actually 0.34 K. Are you doing some sort of annealing <br>> protocol? Again, it's best to give complete information :)<br>> <br>> Nose-Hoover is a poor choice for initial equilibration, if this is what you are <br>> doing. It allows greater temperature fluctuation. Start with Berendsen or <br>> V-rescale for some time, then switch to N-H when collecting your "real" data, if <br>> N-H is your choice for thermostat.<br>> <br>> Is a .trr ever output? If it is, you can view the trajectory to see where <br>> things are going wrong. If you don't get a .trr, then set nstxout = 1 in the <br>> .mdp file to hopefully get a frame or two of where the problem may lie.<br>> <br>> -Justin<br>> <br>> > > 5. Which Gromacs version you are using<br>> > <br>> > I use GROMACS 4.0.3<br>> > <br>> > Thank you<br>> > Antonia<br>> > <br>> > > Date: Wed, 1 Apr 2009 06:39:17 -0400<br>> > > From: jalemkul@vt.edu<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] (no subject)<br>> > ><br>> > ><br>> > ><br>> > > Antonia V. wrote:<br>> > > > Hello,<br>> > > ><br>> > > > I am trying to simulate a system at the NVT ensemble, but after a few<br>> > > > steps I get the error<br>> > > > [compute-0-4:01361] *** Process received signal ***<br>> > > > [compute-0-4:01361] Signal: Segmentation fault (11)<br>> > > > [compute-0-4:01361] Signal code: Address not mapped (1)<br>> > > > [compute-0-4:01361] Failing at address: 0x1913c280<br>> > > > [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70]<br>> > > > [compute-0-4:01361] [ 1] mdrun [0x6a46cd]<br>> > > > [compute-0-4:01361] *** End of error message ***<br>> > > > Segmentation fault<br>> > > ><br>> > > > Any ideas what this means??<br>> > > ><br>> > ><br>> > > Given this information, no. Segmentation faults are difficult to pin <br>> > down,<br>> > > anyway, but if you want help, you'll have to provide more useful <br>> > information:<br>> > ><br>> > > 1. A description of your system<br>> > > 2. Anything else that was printed to screen or the .log file (that's <br>> > where the<br>> > > real error message will appear)<br>> > > 3. What happened in the EM procedure?<br>> > > 4. What .mdp parameters you are using<br>> > > 5. Which Gromacs version you are using<br>> > ><br>> > > -Justin<br>> > ><br>> > > > Thank you<br>> > > > Antonia<br>> > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > What can you do with the new Windows Live? Find out<br>> > > > <http://www.microsoft.com/windows/windowslive/default.aspx><br>> > > ><br>> > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > ><br>> > > > _______________________________________________<br>> > > > gmx-users mailing list gmx-users@gromacs.org<br>> > > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > > Please search the archive at http://www.gromacs.org/search before <br>> > posting!<br>> > > > Please don't post (un)subscribe requests to the list. Use the<br>> > > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > ><br>> > > --<br>> > > ========================================<br>> > ><br>> > > Justin A. Lemkul<br>> > > Graduate Research Assistant<br>> > > ICTAS Doctoral Scholar<br>> > > Department of Biochemistry<br>> > > Virginia Tech<br>> > > Blacksburg, VA<br>> > > jalemkul[at]vt.edu | (540) 231-9080<br>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> > ><br>> > > ========================================<br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before <br>> > posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the<br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > ------------------------------------------------------------------------<br>> > check out the rest of the Windows Live™. More than mail–Windows Live™ <br>> > goes way beyond your inbox. More than messages <br>> > <http://www.microsoft.com/windows/windowslive/><br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> ICTAS Doctoral Scholar<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />check out the rest of the Windows Live™.
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