Dear Gromacs users I am solvating my molecule ( a ploymer chain, having 78 atoms) in Propan-2-one [ molecules] = acetone. I have already updated [ molecules ] section in the topology file (topol.top) after the solvation step.
after the sucessful energy minimization step, while runing grompp I am geting an error, " Excluding 3 bonded neighbours molecule type 'Other' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'acetone' turning all bonds into constraints... Setting gen_seed to 3080450167 Velocities were taken from a Maxwell distribution at 300 K Removing all charge groups because cutoff-scheme=Verlet Fatal error: Atom 79 in multiple T-Coupling groups (1 and 2) " The error means that T-coupling is treating both the polymer (other) and solvent (acetone) as other molecules. How can I rectify the error ? *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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.