[gmx-users] Errors when running SMD, in three direction pulling

[Yukun Wang]

Hi all:
I put three small molecules in the center of an POPC bilayer membrane,and
equilibriated this system in NPT ensemble for 10ns with the position
restriction of small molecules. Then I want to give each of those molecules
an external force to push them away from the center. the force vecters are
on the plane of membrane.
   I realize this using the SMD of Gromacs 4.5.3. But system was very
unstable:
              When using pull=umbrella, after 1000~2000steps the small
molecules in the membrane was shifted along the X-axis or Y-axis very fast,
              When using pull=constraint,after 1000~2000steps the system was
exploded, and serval atoms were shot out of system.
The mdp file of SMD is below:

pull_constr_tol          = 1e-6
pull_geometry            = direction
pull_start               = yes
pull_nstxout             = 50
pull_nstfout              = 50
pull_ngroups            = 3
pull_group0              = ref  ; the whole membrane which is on the plane
of xy
pull_group1              = phe1   ; one of the small molecule
pull_vec1                = -0.866 -0.5 0
pull_rate1               = 0.001             ; [nm/ps]
pull_init1               =
pull_k1                  = 1000             ; [kJ.mol-1.nm-2 /
[kJ.mol-1.nm-1]]
pull_group2              = phe2
pull_vec2                = 0 1 0

pull_rate2               = 0.001             ; [nm/ps]
pull_init2               =
pull_k2                  = 1000             ; [kJ.mol-1.nm-2 /
[kJ.mol-1.nm-1]]
pull_group3              = phe3
pull_vec3                = 0.866 -0.5 0
pull_rate3               = 0.001             ; [nm/ps]
pull_init3               =
pull_k3                  = 1000             ; [kJ.mol-1.nm-2 /
[kJ.mol-1.nm-1]]

and the time step:  dt = 0.001  ; 1 fs

Is there anyone could give me an suggestion for this?
Thank you very much!


Yorquant Wang
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