Dear gmx-users, I have a problem concerning LINCS crashes after transfering a simulation into parallel mode. Due to inherent errors in GROMAS 3.3.2 positional restraints applied on multiple molecules of the same kind could not be handled in parallel and I did the initial part of the simulation in serial mode as suggested by some of the gromacs user. However, due to time restraints and computational resourses I would like to conduct the rest of the simulation in parallel without the positional restraints, of course. I prepared a *.trp file using the -shuffle and -sort options but at the very beginning of the run the LINCS crashed. My system consists of 81 DPPC molecules and 8280 water molecules. The errors in the constraints always appeared to originate from water molecules. I tried many ways to get around the problem. First, I united the lipids into one molecule but thi did not help. I reduced the time step to 1 fs or made use of other (not the latest) points to continue the unrestrained trajectory but all the efforts were in vain. Also, I switched off the -shuffle and -sort options as I read that sometimes they could cause run crashes.
Have somebody else encountered such an issue and if so, could he/she propose how to tackle the problem. Best wishes, Philip
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