[gmx-users] constraint pull code causes crash
chengdi123000 at gmail.com
Sat Apr 3 04:00:34 CEST 2010
My intention is to pull a group of silica to a membrane and output the
force act upon the silica.
I used the pull code as below:
pull = constraint
pull_geometry = direction
pull_start = yes
;pull_dim = N N Y
pull_nstxout = 500
pull_nstfout = 500
pull_ngroups = 1
pull_group0 = DOPC
pull_pbcatom0 = 4958
pull_group1 = MOL;silica
pull_init1 = 0.0
pull_vec1 = 0.0 0.0 -1.0
pull_rate1 = 0.01
;pull_k1 = 5000
I found using constraint always crash. some times a water cannot be
settled. some times no error info output just crash.
So I used an umbrella method to pull the silica, and a pull_K1 = 5000
is used. The mdrun went well. However, the traj is strange. At start
the silica does not move, and suddenly it accelerate to more than 0.01
nm/ps can penetrate the membrane.
Anyone could help me? Thanks.
University of Science and Technology of China
Hefei, Anhui Province 230026
P. R. China
E-mail: chengdi at mail.ustc.edu.cn
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