[gmx-users] Re: Steered Molecular Dynamics (SMD) in Gromcas-4.0.5(toby10222224 at sina.com)

[Justin A. Lemkul]

toby10222224 at sina.com wrote:
> Hi Carsten:
> 
> Thank you for your answers. I don't know whether I am right to reply to 
> gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>. If I am wrong, 
> please tell me.
> 

Yes, keep all discussions on the list for archival purposes (plus, other users 
can weigh in with advice).

> As in my last letter, I said I was not able to set "*pull_weights1*" 
> correctly. I have red the mannual, but I don't understand what it tells. 
> I'll do with your recommendation, setting one pull group which contains 
> 700 atoms and using Gromacs-4.0.7. Then how to set the "*pull_weights1*" ?
> 

If you have a single pull group with 700 atoms, then you can leave pull_weights1 
alone - leave it to its default value (which I believe is 0) by not even 
specifying it in the .mdp file.

-Justin

> Best regards!
> 
>  
> 
>  
> 
> Hi,
> 
> you should set one pull group, not 700. The number of atoms in your
> pull group is 700. Freezing the pull group in x and y direction probably
> does what you want. Please also consider to upgrade to 4.0.7,
> which is the most recent stable version.
> 
> Best,
>   Carsten
> 
> 
> On Jan 22, 2010, at 7:41 AM, toby10222224 at sina.com wrote:
> 
>  > Dear all:
>  >        I’m using Gromacs-4.0.5 and I want to use the pull code to pull a slab of griphene to move along the Z direction in the simulation (Steered Molecular Dynamics-SMD). The griphene has 700 carbon atoms and the positions of the 700 atoms are expected to be immobile in the X and Y direction.
>  > The following is the PULL CODE in my mdp file. However, when I used this code for my simulation the error always came out as “Number of weights (1) for pull group 1 'sla' does not match the number of atoms (700)”.
>  > So here are my doubts about this simulation:
>  > 1.       Can Gromacs-4.0.5 do this for me, especially keeping the C atoms immobile in X and Y direction while moving along the Z direction?
>  > 2.       In my simulation, every carbon atom in the slab of griphene was defined as a group. Is it right?
>  > 3.       How to give the “pull_weights1” to avoid the above ERROR?
>  > Any suggestions and answers are welcome. Thank you in advance!
>  >  
>  > ; COM PULLING          
>  > ; Pull type: no, umbrella, constraint or constant_force
>  > pull                     = constant_force
>  > ; Pull geometry: distance, direction, cylinder or position
>  > pull_geometry            = distance
>  > ; 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                  = 
>  > ; Switch from r1 to r0 in case of dynamic reaction force
>  > pull_r0                  = 
>  > pull_constr_tol          = 1e-06
>  > pull_start               = no
>  > pull_nstxout             = 10
>  > pull_nstfout             = 10
>  > ; Number of pull groups 
>  > pull_ngroups             = 700
>  > ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)
>  > pull_group0              = 
>  > pull_weights0            = 
>  > pull_pbcatom0            = 
>  > pull_group1              = sla
>  > pull_weights1            = 1
>  > pull_pbcatom1            = 0
>  > pull_vec1                = 0.0 0.0 1.0
>  > pull_init1               = 0.0
>  > pull_rate1               = 0
>  > pull_k1                  = 1.2e-4
>  > pull_kB1                 = 0
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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