Hello-
I am running some simulations using time-average J-coupling restraints, and
I have a few questions:
1. Is VALUE1 for TORAVE (which sets the value of tau for the exponential
decay) in picoseconds? Or is it timesteps?
2. I am writing the value that is being restrained to a file, ring.out,
every 1000 timesteps (see input file and restraint file below). When I
average the values in ring.out, the coupling constant I obtain is 0.3 Hz
lower than when I average over the entire simulation. For the average over
the simulation, I am grabbing the value of the dihedral angle using ptraj,
then I'm calculating the coupling constants from those dihedral angles and
averaging using a python script. So, my question is, what is the value that
is being written out to ring.out? Is it the instantaneous value of the
coupling constant, or the time-averaged value?
Thank you in advance for any advice or suggestions.
Input file:
***********************************************************
Dynamic Simulation with solvent box
# Control section
&cntrl
ntwr = 1000, ntwx = 1000, ntpr = 100,
ntt = 1, temp0 = 300.0, tempi = 300.0, tautp = 1.0,
scnb = 1.0, scee = 1.0, dielc = 1, cut = 8.0,
ntb = 2, ntc = 2, ntf = 2,
nstlim = 25000000, t=0.0, dt = 0.0020,
ntp = 1, taup = 0.1,
imin = 0, irest = 1, ntx = 5, iwrap = 1, nmropt = 1,
&end
&ewald
skinnb = 1.0,
nbflag = 1,
&end
&wt
type='TEMP0', istep1 = 1, istep2 = 25000000, value1 = 300.0, value2 =
300.0,
&end
&wt type='TORAVE', value1=5000, value2=1, /
&wt type='DUMPFREQ', istep1=1000, /
&wt type='END' /
DISANG=ring.rst
DUMPAVE=ring.out
&wt
type='END'
&end
&rst IAT(1) = 0 &end
END
***********************************************************
Restraint file:
***********************************************************
# 963 atoms read from pdb file x-83_sol.pdb.
# 1 0LD JNU1: (1 0LD H1)-(1 0LD C1)-(1 0LD C3)-(1 0LD H5) 4.3 4.7
&rst iat = 2, 1, 8, 9,
r1 = 3.3, r2 = 4.3, r3 = 4.7, r4 = 5.7,
rjcoef = 7.29, 0.16, -0.23,
rk2 = 1.0, rk3 = 1.0, &end
***********************************************************
--
With best regards,
--Mickey Richards
Department of Chemistry
University of Alberta
email: mickey18385.gmail.com
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Received on Wed Oct 27 2010 - 11:30:03 PDT
