On 5/31/15 8:37 AM, soumadwip ghosh wrote:
Thank you very much for your help Justin. I really appreciate I would like to bother you for one last time ( as of now ;). So, if I am dealing with a non-trivial molecule like CNT or some polyelectrolyte and I mainly intend to demonstrate the non-bonding interactions with some nucleic acids (say a CNT-dsDNA ) interaction, it appears to me that I dont need to care about the DNA topology even if it lacks the said parameters but I do have to care about these while updating the cnt.itp files since grompp complains about the missing parameters in the cnt.itp file. If one does not write the [ atomtypes ] and the [ pairtypes ] sections in the cnt.itp file and misses out the sigma and epsilon terms I think it underestimates the non-bonding energy terms of interaction between DNA bases and CNT atoms in the md.edr file to some extent. I will appreciate your opinion on this statement.
That doesn't make sense. If you are missing parameters, grompp will complain and fail with a fatal error. If grompp happily carries on and produces your .tpr, then you're getting the interactions the force field dictates because grompp found everything the molecules need in ffbonded.itp, ffnonbonded.itp, or specified in a molecule .itp. If you override grompp's messages with -maxwarn, well then that's your fault :)
Also note that [pairtypes] are intramolecular terms. They do not affect DNA-CNT interactions.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
