[gmx-users] deform option for shear simulation of monoatomic fluids - incorrect velocity profile

Kumar V musthafa84 at gmail.com
Tue Dec 18 10:06:12 CET 2007

Dear All,
              I am using GROMACS to conduct Non-equillibrium MD on coarse
grained water (Parameters from S J Marrink) and also SPC water using DEFORM
option (Kind of Lees-Edwards boundary conditions). I used different
deformation rates from 0.005 to 0.05 for XZ plane. But my  problem is that I
am unable to get the linear velocity profiles. I am using equilibrated
configurations from NPT simulations as an input to Non equilibrium NVT
simulations with berendsen temperature coupling. I don't know why I am
unable to get linear velocity profiles along z direction.  I used g_traj for
getting velocities and coordinates in desired directions. And then I wrote
my own C routine for checking the velocity profile. Can anyone help here
regarding this? Or am I missing something here?

Thanks and Regards,
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