Hi, I am using freeze groups to hold the x, y, and z positions of specified atoms fixed (to roughly simulate a fixed surface). I would like to keep the positions of atoms of residuetypes "AT1" and "AT2" fixed. So, in my .mdp file, I have the following keywords pertaining to "freeze":
freezegrps = AT1 AT2 freezedim = Y Y Y Y Y Y ; freeze x, y & z directions When I run the simulation, I observe that the positions of the "frozen" atoms change significantly. For example, suppose I consider the x-position of atom 2 (which is of residuetype "AT1" and is thus frozen). In my input file, conf.g96, I have the following entry for atom 2: 1 AT1 CP 2 0.353750000 0.061271297 11.700000000 So, the x-position of atom 2 is 0.353750000 nm. Then I run my simulation (in double precision) using grompp_d followed by mdrun_d. I save configurations every timestep (my timestep is 1 fs), using nstxout = 1, and I use the NVT ensemble (using tcoupl = nose-hoover, tc_grps = system, ref_t = 350, and tau_t = 1.0). Then, I use "g_traj_d -f my.trr -s my.tpr -n my.tpr -ox my.xvg -fp -noy -noz" to extract only the x-position of atom2 and print these values to an .xvg file. I obtain the following: 0 3.56560087860643e-01 0.001 3.57711670093127e-01 0.002 3.58265131434284e-01 ... 0.011 3.60305324395584e-01 0.012 3.60525009903859e-01 ... 0.021 3.63643322576657e-01 0.022 3.64169229293184e-01 ... 0.041 3.76755705048180e-01 0.042 3.77036248430013e-01 ... 0.05 3.78067513842026e-01 0.051 3.78112854943937e-01 ... 0.101 3.78302201368430e-01 0.102 3.78302202249019e-01 ... 0.501 3.78302205990565e-01 0.502 3.78302205990565e-01 ... 0.71 3.78302205990565e-01 0.711 3.78302205990565e-01 ... 0.911 3.78302205990565e-01 0.912 3.78302205990565e-01 ... and so on over time (the value converges to 3.78302205990565e-01 nm). I have two questions, if you have time: (i) Why is the x-position of atom2 at time t = 0 ps "3.56560087860643e-01 nm" rather than something slightly closer to the value given in conf.g96 ("0.353750000 nm")? However, this discrepancy at time t = 0 ps is not all that bad; the discrepancy is about 0.0028 nm. (ii) Why does the x-position of atom2 drift drastically over time, until it appears to converge to "3.78302205990565e-01 nm"? This discrepancy seems very significant (a drift of about 0.0245 nm from the initial x-position). A drift of ~0.02 nm for my "frozen atoms," since the bond length between adjacent frozen atoms is 0.1415 nm. Why does this drift happen, and why does it converge to a single (incorrect) value, even when I run several nanoseconds? Do you have any thoughts about why my atoms are not remaining frozen? Is there anything else I can try? I checked the y- and z-components other atoms, and their drifts are of the same order of magnitude. Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- 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