This error occurs because the shortest distance will be used for analysis. There are 2 distances, the linear distance between group 0 and group 1, the other distance passes outside the PBC and enters on the otherside, at the backside of group0. Your box is too small, increase the distance of the length which the force is being applied (Z i e tutorial). ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Agnivo Gosai [agnivogromac...@gmail.com] Sent: Wednesday, November 26, 2014 8:44 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] SMD - Pulling Error in mdrun 0.49 times box size
Dear Users I have put my molecule complex in a box having dimensions 7.5 7.5 15 . The center of the molecule is fixed as 3.75 3.75 and 4.0. I use pull geometry = distance. I did the following SMDs keeping pull force constant unchanged : 1. 500 ps SMD with pull rate = 0.01 nm / ps. mdrun successfully completed. nsteps = 250000 dt = 0.002 2. 1 ns SMD with pull rate = 0.005 nm / ps. mdrun successfully completed nsteps = 500000 dt = 0.002 3. 5 ns SMD with pull rate = 0.001 nm / ps. nsteps = 2500000 dt = 0.002 . Error after the 2383000 th step Distance of pull group 1 (7.306606 nm ) is larger than 0.49 times the box size ( 7.455605 ). You might want to consider using "pull-geometry = direction-periodic" instead. I also noticed that the "distance at start " for pull group 1 = 2.560 in grompp output. Initially I thought that this distance plus 5 nm (the total pulling distance) > 0.49 times 15 nm ( length of box in z direction ) and is contributing to the error. But this has been the same in cases 1 and 2 also. Hence I am getting confused. Any suggestions , please ?? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- 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. This email may be confidential and subject to legal privilege, it may not reflect the views of the University of Canterbury, and it is not guaranteed to be virus free. If you are not an intended recipient, please notify the sender immediately and erase all copies of the message and any attachments. Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more information. -- 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.
