Hello GROMACS users, I'm doing MD for nitrogen, and for better electrostatic interactions I need to use massless and charged virtual site. I did that but when I try to do energy minimization gives me LINCS warning and crush. I don't know where is the error I tried a lot but could not find a solution. Anyone has an idea where is my error
Here is the topology file (hand written) ------------------ [ defaults ] 1 3 yes 0.5 0.5 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; [ atomtypes ] ; name bond_type mass charge ptype sigma epsilon OP OP 0.000 0.000 A 0.330 0.3062 ; nitrogen M M 0.000 0.000 V 0.000 0.000 ; virtual site ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; [ moleculetype ] ; name nrexcl N2 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 OP 1 N2 N1 1 -0.482 14.0067 2 M 1 N2 M1 1 0.964 0.000 3 OP 1 N2 N2 1 -0.482 14.0067 [ constraints ] ; the N-N is fixed 1 3 1 0.11 [ virtual_sites2 ] ; site ai aj funct a 2 1 3 1 0.5000 ; right in the mid ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; [ system ] N2 in vacuo [ molecules ] N2 1500 ------------------------------------------------------------ -------------------------------------- Here is the structure (N2.pdb) ----------- TITLE N2 with dummy masses REMARK THIS IS A SIMULATION BOX MODEL 1 COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.2 CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 ATOM 1 N1 N2 1 0.000 0.000 0.000 1.00 0.00 N ATOM 2 M1 N2 1 0.55000 0.000 0.000 1.00 0.00 Xx ATOM 3 N2 N2 1 1.100 0.000 0.000 1.00 0.00 N CONECT 1 3 CONECT 3 1 MASTER 0 0 0 0 0 0 0 0 3 0 3 0 END0 ------------------------------------------------------------ --------------------------------- Thank you -- 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.