Fatemeh Ramezani On Sunday, 12 March 2017, 20:16, fatemeh ramezani <fr_...@yahoo.com> wrote:
Hi I have a system of protein-gold-ions-water to simulate. The force field which I use, is Golp-charmm. In this force field two au atoms with mass 0.5 and charge 0.3 (AUC) rotates around the main au atoms (with mass 196.967 and charge -0.3: AUS)that are freezed during the simulation. from the beginning of em step, I get LINCS-warning as follow: Step 10, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.355795, max 10.124834 (between atoms 23842 and 23841) bonds that rotated more than 90 degrees: atom 1 atom 2 angle previous, current, constraint length 23842 23841 171.4 0.0700 0.7787 0.0700 22137 22138 171.5 0.0700 0.7786 0.0700 21466 21465 133.5 0.0700 0.0996 0.0700 Step 10, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.196701, max 10.123523 (between atoms 22137 and 22138) bonds that rotated more than 90 degrees: atom 1 atom 2 angle previous, current, constraint length 22137 22138 171.5 0.0700 0.7786 0.0700 23770 23769 172.7 0.0700 0.7763 0.0700 When I checked the warning, I see the first warning is related to 2 AUC and AUS atoms.but according to the force field setting it is necessary to AUC atoms rotate around the AUS.How can change the lincs warning threshold? can you help me to solve the problem? Anybody may help me? Your suggestions would be appreciated. Thanks in advance. Sincerely, Fatemeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.