Quoting Magnus Andersson <[EMAIL PROTECTED]>: > Hi all, > > My constrained 20ps simulation crashes for some reason. This simulation is > very much alike other simulations I've run in a successful manner > previously. Seems like there is a probem on atoms constituting an > artificial membrane... > > Anyway, I guess it is a general question. Where do you start looking if > the run crashes like this (and a slightly different system, just strctural > change, it has exactly the same atoms...)? > > Error message looks like= > > step 340, will finish at Tue Dec 11 12:52:51 2007 > Step 344, time 0.688 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 0.000822 (between atoms 2262 and 2263) rms 0.000041 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 2262 2263 42.4 0.1090 0.1089 0.1090 > 2265 2266 30.3 0.1090 0.1090 0.1090 > > Step 345, time 0.69 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 0.001312 (between atoms 2265 and 2266) rms 0.000051 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 2262 2263 30.0 0.1089 0
In my experience, looking at the atoms LINCS is complaining about is a good place to start. I've seen these warnings when I have somehow generated a structure with bad contacts. Thorough energy-minimization and gentle equilibration usually alleviates the problem. -Justin > > Thankful for a reply / > > Magnus Andersson > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
