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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