Dear all, I have met a problem in my simulation, where I hope to remove the center of mass of one group, namely CNT02, and to pull another group by a constant force. My mdp file reads:
; Remove center of mass translation comm_mode = Linear nstcomm = 10 comm_grps = CNT02 ; COM pulling pull = constant_force pull_geometry = direction_periodic pull_ngroups = 1 pull_group1 = CNT05 pull_vec1 = 0.0 0.0 1.0 pull_k1 = 10 ; kJ / mol / nm The COM pulling has worked, as the Z position of CNT05 was continuously increasing/decreasing along the force direction. However, I found the program has removed the COM of the whole system, rather than of the group CNT02. Let me use "g_traj -com -ox coord.xvg" to extract the COM information, Group 0 ( System) has 57608 elements Group 1 ( Other) has 57608 elements Group 2 ( CNT01) has 3032 elements Group 3 ( CNT02) has 3032 elements Group 4 ( CNT03) has 3032 elements Group 5 ( CNT04) has 3032 elements Group 6 ( CNT05) has 3032 elements Group 7 ( CNT06) has 3032 elements Group 8 ( CNT07) has 3032 elements Group 9 ( CNT08) has 3032 elements .... If 0 was selected, such coord.xvg was generated @ title "Center of mass" @ xaxis label "Time (ps)" @ yaxis label "Coordinate (nm)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "System X" @ s1 legend "System Y" @ s2 legend "System Z" 0 10 10 17.3113 0.2 10 10 17.3113 0.4 10 10 17.3113 0.6 10 10 17.3113 If 3 was selected, for CNT02, the COM was not a constant, i.e., CNT02 was moving all the time. @ s0 legend "CNT02 X" @ s1 legend "CNT02 Y" @ s2 legend "CNT02 Z" 0 11.7971 10.2633 17.5756 0.2 11.7966 10.2602 17.5768 0.4 11.7928 10.2594 17.5783 0.6 11.789 10.2582 17.5799 0.8 11.7856 10.2552 17.5817 1 11.7831 10.2547 17.5837 1.2 11.7828 10.2554 17.586 1.4 11.7846 10.2562 17.5884 1.6 11.7891 10.2582 17.5909 1.8 11.7942 10.2621 17.5934 Best Regards xiaohua -- Xiaohua Zhang Suzhou Institute of Nano-Tech and Nano-Bionics Ruoshui Road 398, Suzhou 215123, China Phone: +86 512 62872552 Mobile: +86 137 71904040 Email: zhan...@fudan.edu.cn Email: xhzhang2...@sinano.ac.cn -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
