Dear all,
I am trying to do umbrella sampling considering two reaction coordinates: increase one N-H bond length (from 1.1A to 1.8A) and decrease one O-H bond (from 1.8 to 1.1A) (which are part of the substrate PPD). To do the same I use the following input for equilibration step.
10 ps equilibration run
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
ntc = 2,
noshakemask = ":PPD"
ntf = 2,
cut = 10,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000, dt = 0.001
ntpr = 100, ntwx =100, ntwr =200
nmropt = 1, ioutfm=1
/
&wt
type='END',
&end
DISANG=comb7
The comb7 file:
Two restraints N-H and O-H
&rst
iat=12230,12245
r1=0.0, r2=1.7, r3=1.7, r4=10.0,
rk2=1000, rk3=1000
&end
&rst
iat=12219,12245
r1=0.0, r2=1.2, r3=1.2, r4=10.0,
rk2=1000, rk3=1000,
&end
When I increase N-H bond length from 1.1 upto 1.6, there was no problem. When I set it 1.7 as given in the above input file it gives the following error.
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 3 4945 10018 10019
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
How to solve this problem. Please let me know.
With best regards
Sindrila
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Received on Wed Jul 10 2013 - 22:00:03 PDT
