[gmx-users] umbrella sampling with "pull=constraint"

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Nov 7 15:07:21 CET 2011

Dear Vijay:

Can you please provide evidence for your claim that the harmonic  
potential is not applied properly, since you may decide to use  
pull=umbrella once you have set that up correctly. Importantly,  
movement out of the unit-cell is not a problem, as discussed a lot on  
this list. Nevertheless, you do need to worry about which images are  
used to derive the pulling forces. You can often do that by a  
judicious selection of pull_pbcatom (read about that on-list and in  
the manual). In some cases, however, pull_pbcatom can not assist  
enough and you are forced to make the box larger. None of this is  
alleviated by pull=constraint, which is why I'm not going to answer  
your question about your .mdp parameters at this point. Let's get the  
problems identified and solved first with pull=umbrella.


-- original message --


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


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