I used amb2gmx.pl (from http://chemistry.csulb.edu/ffamber/) to convert an amber topology and restart file to a gromacs topology and structure file and tried to continue the simulation in gromacs. I got the following error message:
Constraint error in algorithm Lincs at step 0 t = 0.000 ps: Water molecule starting at atom 4642 can not be settled. Check for bad contacts and/or reduce the time-step. Wrote pdb files with previous and current coordinates It seems strange to me that this error occurs as there was no problem with this simulation in amber. (it ran a few ns in amber). I tried to run it after minimalization and this worked fine. So there seems to be a problem while converting the files, I am new to gromacs and I don't really have a clue how to find the cause of this problem, perhaps some of you also tried to continue a amber run in gromacs? kind regards, servaas michielssens _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
