I already decrease it to 0.002 as you said and then there comes this error I wrote to you. Now It try it with 0.001. It is still running.
Thank you for your answer. Eva > > > On 7/9/12 9:46 AM, [email protected] wrote: >> With the mentioned below options I get the following error: >> >> Fatal error: >> 1 particles communicated to PME node 1 are more than 2/3 times the >> cut-off >> out of the domain decomposition cell of their charge group in dimension >> x. >> This usually means that your system is not well equilibrated. >> >> >> But it does not occur immediatly but only at step >> >> Step 695, time 1.39 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 2.011725, max 78.611298 (between atoms 3778 and 3781) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 3782 3785 92.2 1.3061 0.2785 0.1090 >> 3782 3784 93.0 0.1055 0.2552 0.1090 >> 3782 3783 91.0 0.1062 0.3086 0.1090 >> 3204 3206 89.6 0.1449 1.0256 0.1449 >> 3204 3205 89.7 0.1010 0.9949 0.1010 >> >> >> Is there something wrong with my temperature coupling? >> > > I doubt it. Decrease your timestep (as I've said twice now) and try again > with > something sensible for dt. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
