[gmx-users] constraint pull code causes crash

程迪 chengdi123000 at gmail.com
Sat Apr 3 04:00:34 CEST 2010

Hi, gmxusers

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.

Di Cheng

University of Science and Technology of China
Hefei, Anhui Province 230026
P. R. China
E-mail: chengdi at mail.ustc.edu.cn
Tel.: +86-15321055911

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