Dear Justin Thank you for previous reply. I am doing Carbon nano tubes Wrapped by Cyclic peptide After 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 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 step 141: Water molecule starting at atom 106721 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Segmentation fault So I Have reduced the Time step Again I have received the same error as follows but this time Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Segmentation fault How to Avoid Should I Equilibrate for Longer time? . I Have done 2ns Equilibration Only Is My equilibration is not enough? Thanks In Advance -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
