Hello, I have done umbrella sampling with "pull=umbrella" and I found that the pulling group has high fluctuations and sometimes moving out of the periodic box. I think that the harmonic potential is not properly applied and thus the pulling group is not retained with the specified COM distance between the reference and pulling group. Can we use pull=constraint option to retain the pulling group within the COM distance? my pulling code is as bellow with restrain at 0.5nm distance from ref group. I just want to get some idea about this pull code modification.
pull = constraint pull_geometry = distance pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group0 = Chain_A pull_group1 = Chain_B pull_init1 = 0.50 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout = 500 pull_nstfout = 500 Regards, Vijay.
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