Please don't hijack an unrelated thread with a new question. I am re-titling this message; in the future, just send a new email when you have a new question.
On 4/27/14, 11:11 AM, Swetha Srinivasan wrote:
Hi Lemkul, I am trying to simulate guanidium in water. My system contains 198 guanidium residues. But when I'm trying to use the grompp command ,I'm facing the problem of fudgeQQ, qi ,qj. I don't know what that means. I don't know how to rectify the error too. Plus if there are too many solvet molecules, how do I delete it ?
FudgeQQ is explained in the manual. Beyond that, you need to provide more details. What is in your topology? Did you create it yourself, or did you get it from some other source? What is the *exact* error message from grompp (copied and pasted from the terminal)?
As for solvent removal, you'll have to tell us how you added solvent in the first place. Presumably this was done with genbox, in which case you can use -maxsol, but that's often not a good idea because it will leave voids in the simulation box. If the box is too large, you'll have to set up an appropriate one with editconf (or possibly genbox, but I'm still guessing here because you haven't provided any of your commands).
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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.
