From: Bala subramanian (bala.biophysics_at_gmail.com)
Date: Tue Nov 29 2016 - 09:39:39 CST
Friends,
My aim is the following, a) Study the pmf of a single potassium ion through
a channel, b) Study the pmf of a single potassium ion in the presence of
additional ion. The objective is to calculate the force (along the reaction
coordinate) on my testing ion in the absence and presence of additional
ion, and also the PMF profile.
colvarsTrajFrequency 500
colvarsRestartFrequency 500
colvar {
name Translocation
width 0.2
lowerboundary -4.0
upperboundary -1.0
lowerwallconstant 20.0
upperwallconstant 20.0
distanceZ {
main {atomnumbers { 16625 } # My testing ion
ref { atomnumbers { 2025 7565 13105 }
}
axis ( 0.0, 0.0, 1.0 ) }
}
colvar {
name Additional
width 0.2
lowerboundary -9.0
upperboundary -7.0
hardLowerBoundary yes
hardUpperBoundary yes
lowerwallconstant 20.0
upperwallconstant 20.0
distanceZ {
main { atomnumbers { 16624 } # additional ion from my testing ion
}
ref { atomnumbers { 16625 }
}
axis ( 0.0, 0.0, 1.0 )
}
}
abf {
colvars Translocatio
fullSamples 800
historyFreq 500
}
a) Which is the correct colvar option that I should choose to obtain the
correct force on my testing ion *OutputTotalForce* or *oneSiteTotalForce*
b) I am using latest namd version, the manual says that there is a
*subtractAppliedForce* option available, but it is not recommended.
There is also *ouputAppliedforce* option. Should i simply obtain the
totalfoce and subtract the appliedforce to remove any force due to bias ?
Could you please guide which options should I use to achieve my objective.
-- C. Balasubramanian
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:50 CST