Thanks for the help, I think it worked out. Just for the record: For my chain-like molecule ...- C17 - C18 # C19 - C20 - ... (# = triple bond)
I defined C18 and C19 to be virtual sites defined by the positions of C17 and C20: [ virtual_sites2 ] ; Site from funct a 18 17 20 1 0.353365385 19 17 20 1 0.646634615 And constrained the distance between C17 and C20 to be the sum of the three original bonds shown above: [ constraints ] ; index1 index2 funct length(nm) 17 20 1 0.416 However, I had to set the mass of the "non-virtual" particles C18 and C19 to zero, as Gromacs demands virtual sites have no mass. So technically speaking, my molecule has lost weight. I hope that doesn't lead to artefacts, but as of now trajectories are looking good. Regards, Alex > > Maybe this previous post will be of some use: > > http://lists.gromacs.org/pipermail/gmx-users/2009-May/042068.html > > -Justin > > Alexander Bujotzek wrote: >> Dear all, >> I am experiencing some trouble with a small molecule containing a C-C triple bond, using a topology built by PRODRG beta. I intend to use ffG43a2, with a contraint on all bond lengths. >> Energy minization does not converge, as forces on the atoms involved in the bond seem to oscillate (not very high forces, though). >> Position restrained MD fails with LINCS errors, >> and unrestrained MD leads to a blow-up of the system. >> I guess the fault lies in the representation of the triple bond in the topology file, as a derivate of the molecule (with a single bond in the same place) works just fine. >> Excerpt from the itp building block provided by PRODRG beta. The triple bond is supposed to be between carbons 18 and 19: >> [ bonds ] >> ... >> 17 18 2 0.147 3422818.4 0.147 3422818.4 ; CAQ CAR >> 18 >> 19 2 0.122 2309822.8 0.122 2309822.8 ; CAR CAS 20 19 >> 2 0.147 3422818.4 0.147 3422818.4 ; CAT CAS >> ... >> [ angles ] >> ... >> 16 17 18 2 109.5 520.0 109.5 520.0 ; OAP CAQ >> CAR >> 17 18 19 2 180.0 41840001.2 180.0 41840001.2 ; CAQ CAR >> CAS >> 18 19 20 2 180.0 41840001.2 180.0 41840001.2 ; CAR CAS >> CAT >> 19 20 21 2 109.5 520.0 109.5 520.0 ; CAS CAT >> OAU >> ... >> There is no dihedral with 18 and 19 in the middle, but I assume that is correct as triple bonds are not supposed to be "rotatable"? >> What strikes me is the high force constant on the two 180 degree angles... >> may that be a source of error? >> Any help is appreciated! Maybe someone even has a working template of a correct triple bond topology at hand? >> Best regards and thank you for reading >> Alex >> PS: I also checked ffG43a2bon.itp, but I found nothing resembling a C-C triple bond... or maybe it's just the heat in my office. > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- Alexander Bujotzek Zuse Institute Berlin Computational Drug Design Group Tel. : +49 30 84185-234 eMail: [email protected] _______________________________________________ gmx-users mailing list [email protected] http://lists.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
