On 10/6/16 7:13 AM, Kelechi Okoroafor wrote:
Thank you for the tip, Justin. I incorrectly thought that the coordinates and box dimensions were sufficient to preserve the pressure of the system. I shall make a habit of restarting simulations with the checkpoint file rather than .gro files. My sequence of commands were: - gmx grompp -f npt.mdp -c EM.gro -p sys.top -o NPT1.tpr -n index.ndx -maxwarn -1 - gmx mdrun -v -deffnm NPT1 -nb gpu -tunepme - gmx editconf -f NPT1.gro -o NPT1.pdb -c -d 0.00 - gmx editconf -f NPT1.pdb -o NPT1.gro -c -d 0.00 -
If you just want to convert file formats, omit -c -d in your editconf command and nothing will change. By using -d 0.00, you will be adjusting the system size (you will see this by comparing the box vectors in the input and output files). You're ensuring a bad discontinuity by doing this. My recommendation is to always use unmodified files when continuing runs; it's basically bulletproof. If you want a different format for visualization, that's fine, but just use it for visualization. Your original NPT1.gro should have been fine, but having transformed to .pdb while manipulating the box, then back, you're just invalidating anything that was done previously.
-Justin
gmx grompp -f pme.mdp -c NPT1.gro -p sys.top -o NVT1.tpr -n index.ndx -maxwarn -1 - gmx mdrun -v -deffnm NVT1 -nb gpu -tunepme
-- ================================================== 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.
