Dear Justin Thank you for previous reply. I am doing Carbon nano tubes Wrapped by Cyclic peptide .I am sure of that iher is no error in My topology of My system (CNT Wrapped by Cyclic peptide) After Successful NPT and NVT equilibration When i Run Production MD I have got The following Notes in terminal
NOTE 1 [file CNTCYCfull.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file CNTCYCfull.mdp]: You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = Shift (possibly with DispCorr) NOTE 3 [file CNTCYCfull.mdp]: You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = PME-Switch or Reaction-Field-zero NOTE 4 [file gfggZ.top, line 60]: For energy conservation with LINCS, lincs_iter should be 2 or larger. if I ignore the Notes I am Not Able to run . S I have Changed All options Accordingly in .mdp files Then When I run I have got the following errors after few Minutes step 100, will finish Thu Oct 10 18:44:32 2013 Step 153, time 0.0306 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.010047, max 0.158996 (between atoms 875 and 873) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length rms 37613.979597, max 954780.695847 (between atoms 1189 and 1190) 1157 1156 34.0 0.0997 0.1118 0.1000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1171 1158 36.4 0.1542 0.1972 0.1530 1159 1158 34.8 0.1534 0.2022 0.1530 1178 1176 67.6 0.1528 2.4354 0.1530 1179 1177 79.1 0.1533 0.2981 0.1530 1046 1044 35.1 0.1489 0.3847 0.1470 Fatal error: 3 particles communicated to PME node 2 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. For more information and tips for troubleshooting, please check the GROMACS Thanks In Advance -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
