Hi, I am trying to do a simple membrane simulation of a h4 residue helix in DMPC. However, I encounter a strange issue this time when i try to run the final production run. the error that i get is as follows:
Check for bad contacts and/or reduce the timestep. WARNING: Unsupported box diagonal 6.178595 6.197406 -0.367044, will not use periodic boundary conditions WARNING: Unsupported box diagonal 6.178595 6.197406 -0.367044, will not use periodic boundary conditions So i went back and checked the gro file and removed all possible waters or lipid atoms that may have been close to the protein and still it remains the same. My box diagonal as shown in the gro after em is 6.30580 6.32500 8.42100. However,after positional restraint dynamics my coordinates are 6.17859 6.19740 7.87826. I wonder why this change occurs. Thank you for your time. ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ -- 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
