From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Feb 14 2017 - 18:12:38 CST
The distance Z colvar is relative. So the position of main along the z axis relative to ref. If your dummy is where you want it to be, you indeed give 0.
Josh Vermaas
Director’s Postdoctoral Fellow
National Renewable Energy Laboratory
joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>
On Feb 14, 2017, at 11:15 AM, Life Sciences Inc <contact.lifesciences.inc_at_gmail.com<mailto:contact.lifesciences.inc_at_gmail.com>> wrote:
Hi all
I am trying to fix the center of mass of one of my selection in lipid bilayer say phosphate atoms, and my protein which is inserted inside the lipid bilayer in z direction, I want the com of protein selection and lipid bilayer selection to be exactly the same after equilibration of my system, for this purpose I have used colvars , can anyone tell me am I going in the right direction my input for colvar is as follows and also let me know if I am giving 0.0 with centers parameter my protein selection will be at 0 with respect to lipid selection or do I have to give the 7.218 for centers value?
colvarsTrajFrequency 100
colvar {
name d
width 1.0 # typical displacement is set to 1 Angstrom
distanceZ {
ref {
dummyAtom (0.076, 0.416, 7.218) # fixed position for ref atoms from bilayer
}
main {
# group definition: selection of the protein, which I need to move towards the com of the ref selection
psfSegID P1
atomNameResidueRange CA 1-12
}
}
}
harmonic { # Define a moving harmonic restraint
colvars d # acting on 1 colvars
centers 0.0 #
forceConstant 10.0 # unit is kcal/mol/[width]^2
}
Thanks in advance
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