[gmx-users] choosing confs for Umbrella sampling
abhisek.mndl at gmail.com
Fri May 5 08:48:29 CEST 2017
How brief should the equilibration step be after generating configurations ?
I faced a problem in the equilibration of configurations.
The configuration generated after pulling does not look alike after
performing 10ns of equilibration (using npt_umbrella.mdp). The COM distance
b/w protein-ligand seem to increased drastically.
Does it due to longer time of equilibration given ? Happened for almost all
However I used following (pull_rate1=0.0):
; Pull code
pull = umbrella
pull_ngroups = 1
pull_group0 = Protein_chain_A
pull_group1 = ACO
pull_geometry = direction ; simple distance increase
pull_dim = N N Y ; pulling in Z dimension
pull_rate1 = 0.0
pull_k1 = 1000 ; kJ mol^-1 nm^-2
pull_start = yes ; define initial COM distance > 0
pull_vec1 = 0 0 -1
Please help me out here. I'm using gromacs-4.6.
On Fri, May 5, 2017 at 11:30 AM, abhisek Mondal <abhisek.mndl at gmail.com>
> I have generated 400 configurations after performing a pulling simulation
> as per the tutorial. Among them first 160 shows enough COM separation for
> my study.
> My question is that, is it possible or safe not to use all but few of the
> 160 confs for umbrella sampling (as long as I get good correlated
> histogram) ? I mean if I take, say, conf0,conf4,conf8,conf12,....
> conf100,conf110,conf120,...,conf160. Is it safe ?
> If my correlation of umbrella-histogram falters then I can add confs for
> that area later right ?
> Please give me some suggestion regarding the same.
> Thank you.
> Abhisek Mondal
> *Senior Research Fellow*
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
> *Kolkata 700032*
*Senior Research Fellow*
*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*
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