Dear Amber users and developers,
I’m running SMD to evaluate the PMF of a reaction using the following input file:
SMD: LCOD rxn coord
&cntrl
imin=0,
irest=1, ntx=5,
ntb=2, pres0=1.0, ntp=1, taup=1.0,
cut=12.0,
tempi=300.0, temp0=300.0,
ntt=3, gamma_ln=2.0, ig=-1,
nstlim=20000, dt=0.001,
ntpr=20, ntwx=20, ntwr=5000, ioutfm=1,
ntc=2, ntf=2,
ifqnt=1, infe=1
/
&qmmm
qmmask = ':169,196-199',
qmcharge=0,
qm_theory='PM6',
qmshake=0,
qmcut=8.0,
/
&smd
output_file = 'nat_smd25-7.txt'
output_freq = 20
cv_file='cv_nat-7.in'
/
And the cv_file:
&colvar
cv_type = 'LCOD'
cv_ni=4, cv_i = 2947,2647,2650,2647,
cv_nr=2, cv_r = 1.0,-1.0,
npath=2, path = 2.26718,-1.9,
nharm=1, harm = 25.0
/
I wonder which is the minimum number of trajectories that I should run and how to evaluate the PMF (is it just the arithmetic mean of all the values obtained for the total work done?).
Thank you in advance for any insight,
Sincerely,
Ruth
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Received on Mon Sep 24 2018 - 07:00:02 PDT
