[gmx-users] SMD - Pulling Error in mdrun 0.49 times box size
agnivogromacs14 at gmail.com
Tue Nov 25 20:44:20 CET 2014
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 =
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
Grad Student, Iowa State University.
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