[gmx-users] Re: Steered Molecular Dynamics (SMD) in Gromcas-4.0.5([email protected])

toby10222224 Tue, 26 Jan 2010 20:51:34 -0800

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 &nbsp;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&nbsp;using them, the&nbsp;COM of the slab 
of griphene moved at a constant speed, but the 'slab'&nbsp;crashed. 
Because&nbsp;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)&nbsp;and which pull geometry (distance, 
direction, cylinder or position) shall I&nbsp;use? There is no reference group 
in my simulation.&nbsp;Do I need to&nbsp;modify the .gro file?
&nbsp;
Part of the .gro file:
...
&nbsp;4876sla&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C11052&nbsp;&nbsp; 
3.608&nbsp;&nbsp; 0.748&nbsp;&nbsp; 0.237&nbsp; 0.0000 -0.0000&nbsp; 0.0001
&nbsp;4877sla&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C11053&nbsp;&nbsp; 
3.821&nbsp;&nbsp; 0.871&nbsp;&nbsp; 0.237&nbsp; 0.0000 -0.0000&nbsp; 0.0001
&nbsp;4878sla&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C11054&nbsp;&nbsp; 
0.000&nbsp;&nbsp; 0.871&nbsp;&nbsp; 0.237&nbsp; 0.0000 -0.0000&nbsp; 0.0001
&nbsp;4879sla&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C11055&nbsp;&nbsp; 
3.892&nbsp;&nbsp; 0.748&nbsp;&nbsp; 0.237&nbsp; 0.0000 -0.0000&nbsp; 0.0001
&nbsp;4880sla&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C11056&nbsp;&nbsp; 
0.017&nbsp;&nbsp; 0.748&nbsp;&nbsp; 0.237&nbsp; 0.0000 -0.0000&nbsp; 0.0001
&nbsp;4881sla&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C11057&nbsp;&nbsp; 
3.395&nbsp;&nbsp; 1.117&nbsp;&nbsp; 0.237&nbsp; 0.0000 -0.0000&nbsp; 0.0001
&nbsp;4882sla&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C11058&nbsp;&nbsp; 
3.679&nbsp;&nbsp; 1.117&nbsp;&nbsp; 0.237&nbsp; 0.0000 -0.0000&nbsp; 0.0001
&nbsp;4883sla&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C11059&nbsp;&nbsp; 
3.466&nbsp;&nbsp; 0.994&nbsp;&nbsp; 0.237&nbsp; 0.0000 -0.0000&nbsp; 0.0001
&nbsp;4884sla&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C11060&nbsp;&nbsp; 
3.608&nbsp;&nbsp; 0.994&nbsp;&nbsp; 0.237&nbsp; 0.0000 -0.0000&nbsp; 0.0001
&nbsp;4885sla&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C11061&nbsp;&nbsp; 
3.821&nbsp;&nbsp; 1.117&nbsp;&nbsp; 0.237&nbsp; 0.0000 -0.0000&nbsp; 0.0001
&nbsp;4886sla&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C11062&nbsp;&nbsp; 
0.000&nbsp;&nbsp; 1.117&nbsp;&nbsp; 0.237&nbsp; 0.0000 -0.0000&nbsp; 0.0001
...
These are all the carbon atoms of the slab of griphene.
&nbsp;
; COM PULLING&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
; Pull type: no, umbrella, constraint or constant_force
pull&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = constraint
; Pull geometry: distance, direction, cylinder or position
pull_geometry&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
= direction
; Select components for the pull vector. default: Y Y Y
pull_dim&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = N N Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = 1.5
pull_constr_tol&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = 1e-06
pull_start&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = no
pull_nstxout&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = 10
pull_nstfout&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = 10
; Number of pull groups 
pull_ngroups&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)
pull_group0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = 
pull_weights0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
= 
pull_pbcatom0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
= 0
pull_group1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = sla
pull_weights1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
= 
pull_pbcatom1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
= 0
pull_vec1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = 0.0 0.0 1.0
pull_init1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = 0.237
pull_rate1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = 5e-4
pull_k1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = 
pull_kB1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 = 
&nbsp;
Any suggestions are welcome! Thank you in advance!

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[gmx-users] Re: Steered Molecular Dynamics (SMD) in Gromcas-4.0.5([email protected])

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