[gmx-users] Question about drift in positions of frozen atoms
adeyoung at andrew.cmu.edu
Mon May 14 20:44:57 CEST 2012
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:
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
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!
Carnegie Mellon University
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