On 10/2/14 8:50 AM, Anurag Dobhal wrote:
Thanks Justin I m running the command " mdrun -s em.tpr " and I did get the confout.gro file as output. after that I am running the command " perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat " and then again the energy minimization command. " mdrun -s em.tpr" After that I am solvating the system. I did put a local copy of vdwradii.dat in my working directorie and change the value of C from 0.15 to 0.375. I am solvating my system by the command " genbox -cp system_shrink1.gro -cs spc216.gro -o system_solv.gro -p topol.top " after that I am adding the ions in the system by the command " grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr" But now I am getting an error number of coordinates in coordinate file (system_solv.gro, 8218) does not match topology (topol.top, 1956) can you please help what caused this error.
Don't solvate the intermediate steps. It makes no physical sense. Only solvate when you have shrunk the system to an appropriate size based on APL. Regardless, the number of atoms in the system is way too small to be correct for the tutorial system.
-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.