Dear all,
The complex I am trying to simulate has protein ( 10 chains), DNA, and RNA I ran the simulation for 2 us so far but the biological event I want to observe requires a very long MD simulation. I decided to accelerate the sampling using the AWH method. I am not familiar enough with the AWH method or other methods such as umbrella sampling. I have watched the two webinars on AWH but I am still not sure about the mdp options. Attached is the mdp I used and the error I got!
I believed that I need to choose a reference atom for pulling, But on what basis?
pull = yes ; The reaction coordinate (RC) is defined using pull coordinates. pull-ngroups = 12 ; The number of atom groups needed to define the pull coordinate. pull-ncoords = 7 ; Number of pull coordinates. pull-nstxout = 1000 ; Step interval to output the coordinate values to the pullx.xvg. pull-nstfout = 0 ; Step interval to output the applied force (skip here).
pull-group1-name = Protein_chain_A ; Name of pull group 1 corresponding to an entry in an index file. pull-group2-name = Protein_chain_B ; Same, but for group 2. pull-group3-name = Protein_chain_C pull-group4-name = Protein_chain_D pull-group5-name = Protein_chain_E pull-group6-name = Protein_chain_F pull-group7-name = Protein_chain_G pull-group8-name = Protein_chain_H pull-group9-name = Protein_chain_I pull-group10-name = Protein_chain_J pull-group11-name = RNA pull-group12-name = DNA
pull-group1-pbcatom = 0 pull-group2-pbcatom = 0 pull-group3-pbcatom = 0 pull-group4-pbcatom = 0 pull-group5-pbcatom = 0 pull-group6-pbcatom = 0 pull-group7-pbcatom = 0 pull-group8-pbcatom = 0 pull-group9-pbcatom = 0 pull-group10-pbcatom = 0 pull-group11-pbcatom = 0 pull-group12-pbcatom = 0
pull-coord1-groups = 1 2 ; Which groups define coordinate 1? Here, groups 1 and 2. pull-coord2-groups = 3 4 pull-coord3-groups = 5 6 pull-coord4-groups = 7 8 pull-coord5-groups = 9 10 pull-coord6-groups = 11 12 pull-coord7-groups = 11 12
pull-coord1-geometry = distance ; How is the coordinate defined? Here by the COM distance. pull-coord1-type = external-potential ; Apply the bias using an external module. pull-coord1-potential-provider = AWH ; The external module is called AWH!
awh = yes ; AWH on. awh-nstout = 50000 ; Step interval for writing awh*.xvg files. awh-nbias = 1 ; One bias, could have multiple. awh1-ndim = 1 ; Dimensionality of the RC, each dimension per pull coordinate. pull-coord1-groups awh1-dim1-coord-index = 1 ; Map RC dimension to pull coordinate index (here 1–>1) awh1-dim1-start = 0.25 ; Sampling interval min value (nm) awh1-dim1-end = 0.70 ; Sampling interval max value (nm) awh1-dim1-force-constant = 128000 ; Force constant of the harmonic potential (kJ/(mol*nm^2)) awh1-dim1-diffusion = 5e-5 ; Estimate of the diffusion (nm^2/ps),used to initial update size, how quezly the system moves awh1-error-init = 5 ; Estimate of the error of diffusion , used to set initial update size awh-share-multisim = yes ; Share bias across simulations awh1-share-group = 1 ; Non-zero share group index
ERROR 12 [file AWH3.mdp]: When the maximum distance from a pull group reference atom to other atoms in the group is larger than 0.5 times half the box size a centrally placed atom should be chosen as pbcatom. Pull group 12 is larger than that and does not have a specific atom selected as reference atom.
Any advice you could give would be much appreciated
Thank you so much!
Amnah
dear Amnah Alalmaie ,
AWH calculates the free energy along an order parameter of the system. Free energy barriers are overcome by adaptively tuning a bias potential along the order parameter such that the biased distribution along the parameter converges toward a chosen target distribution. The fundamental equation governing the tuning is: log(target) = bias - free energy, where the bias and free energy are initially unknown. Typically the target distribution is simply chosen uniform, such that the bias completely flattens the free energy landscape.
https://manual.gromacs.org/documentation/2018-current/doxygen/html-full/page_awh.xhtml
Regards,
Shafagat
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