Dear all:
These days, I am trying to pull a slab of griphene moving along the Z direction
at a constant speed. The slab of griphene contains 700 atoms. After several
times of E-mail communication with the Gromacs users, the simulation can run.
However, the run didn't produce the results which I expected. Part of my .gro
file and .mdp file are below. By& using them, the COM of the slab of griphene
moved at a constant speed, but the 'slab' crashed. Because not all the carbon
atoms moved at the same speed.
In order to produce the results that I want, which pull type (no, umbrella,
constraint or constant_force) and which pull geometry (distance, direction,
cylinder or position) shall I use? There is no reference group in my
simulation. Do I need to modify the .gro file?
Part of the .gro file:
...
4917sla C11093 1.265 1.609 0.237
4918sla C11094 1.549 1.609 0.237
4919sla C11095 1.336 1.486 0.237
4920sla C11096 1.478 1.486 0.237
4921sla C11097 1.691 1.363 0.237
4922sla C11098 1.975 1.363 0.237
4923sla C11099 1.762 1.240 0.237
4924sla C11100 1.904 1.240 0.237
4925sla C11101 2.117 1.363 0.237
4926sla C11102 2.401 1.363 0.237
...
These are all the carbon atoms of the slab of griphene.
The Pulling Code:
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = constraint
; Pull geometry: distance, direction, cylinder or position
pull_geometry = direction
; Select components for the pull vector. default: Y Y Y
pull_dim = N N Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1 = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0 = 1.5
pull_constr_tol = 1e-06
pull_start = no
pull_nstxout = 10
pull_nstfout = 10
; Number of pull groups
pull_ngroups = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)
pull_group0 =
pull_weights0 =
pull_pbcatom0 = 0
pull_group1 = sla
pull_weights1 =
pull_pbcatom1 = 0
pull_vec1 = 0.0 0.0 1.0
pull_init1 = 0.237
pull_rate1 = 5e-4
pull_k1 =
pull_kB1 =
Any suggestions are welcome! Thank you in advance!
--
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/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/mailing_lists/users.php
