[gmx-users] Re: Steered Molecular Dynamics (SMD) in Gromcas-4.0.5(toby10222224 at sina.com)
Justin A. Lemkul
jalemkul at vt.edu
Sat Jan 23 04:38:01 CET 2010
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.
> Best regards!
> 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.
> On Jan 22, 2010, at 7:41 AM, toby10222224 at sina.com wrote:
> > Dear all:
> > Im 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
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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