On 1/30/14, 2:27 PM, Ozbil, Mehmet wrote:
For Dummy atom, I tried to write DUM for atom type and give 0 charge but it could not recognize the atom type. Then I just wrote the atom type with 0 charge but as I understand I could not make it a dummy atom. How can I do it?
The DUM type has no parameters assigned in ffnonbonded.itp in oplsaa.ff for some reason. You can easily add it; it has zero mass, zero charge, and zeroes for sigma and epsilon.
And also for the parameters, I understand the fact that the bonding and non-bonding interactions will change, but I could not find a good example or I could not understand how to do it? In the manual, Section 5.7.4 there is an example but I don`t understand where the gb_ parameters are coming from:
Unfortunately, the example is for Gromos96, which happens to work differently from all of the other force fields in Gromacs. The gb_*, ga_*, etc are simply macros for copying and pasting parameters from ffbonded.itp. The general form of the topology is always observed; see Table 5.5.
[ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 H 1 PROP PH 1 0.398 1.008 CH3 0.0 15.035 2 OA 1 PROP PO 1 -0.548 15.9994 CH2 0.0 14.027 3 CH2 1 PROP PC1 1 0.150 14.027 CH2 0.0 14.027 4 CH2 1 PROP PC2 2 0.000 14.027 5 CH3 1 PROP PC3 2 0.000 15.035 [ bonds ] ; ai aj funct par_A par_B 1 2 2 gb_1 gb_26 5.7. File formats 135 2 3 2 gb_17 gb_26 3 4 2 gb_26 gb_26 4 5 2 gb_26 [ pairs ] ; ai aj funct 1 4 1 2 5 1 [ angles ] ; ai aj ak funct par_A par_B 1 2 3 2 ga_11 ga_14 2 3 4 2 ga_14 ga_14 3 4 5 2 ga_14 ga_14 [ dihedrals ] ; ai aj ak al funct par_A par_B 1 2 3 4 1 gd_12 gd_17 2 3 4 5 1 gd_17 gd_17 Also here the example for Gromos forcefield but I am using OPLS force field so I assume these numbers will be different as well. How can I find the parameters for B state for OPLS force field?
All of that information is in ffbonded.itp, as it is for all force fields. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
