Dear Mark, thank you very much for prompt reply, I am sorry but I did mistake in my first e-mail I have run an NVE simulation of decamer of glycin first with PBC (coulombtype=PME)and later without PBC (coulombtype=Cut-off). Zuzana
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Thursday, May 03, 2007 3:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Temperature increase Zuzana Benkova wrote: > I have run an NVE simulation of decamer of glycin first with PBC > (coulombtype=Cut-off) and later without PBC (coulombtype=PME). You can't have a non-periodic system with PME. > The > gen-temp was set to 300K with option gen-vel=yes. The temperature start > to raise during simulation and finaly the following messages appeared in > log file > > Shake did not converge in 1000 steps > > i mi j mj before after should be > > 66 14.01 67 1.01 0.10100 0.10318 0.10100 > > Constraint error in algorithm Shake at step 980454 > > Wrote pdb files with previous and current coordinates > > How can I cope with this? We can't tell, because the above description is not self-consistent. In any case you haven't defined your topology, or minimized your structure or equilibrated properly. Then some bad structural element is causing a region to have too much energy which is breaking structures. Search the mailing list archives for suggested equilibration regimes, or read relevant literature examples, or do tutorial material. Mark _______________________________________________ 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 _______________________________________________ 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
