Hi! I have a problem with blowing system on relative free energy
calculation.
I finished tutorial A9 without problem and decided to try simulate some
simple system.
End states of simulation is n-butane and isobutane.
So I prepared starting files and parametrize molecules in antechamber.
I want to do main cycles (minimization -> heating -> pressuring -> md) at
each lambda point of simulation, not only at lambda = 0.5.
My system blew at "lambda = 0.05 decharge stage"
Input files for heating process
HEAT0.in
heating
&cntrl
imin = 0, nstlim = 10000, irest = 0, ntx = 1, dt = 0.002,
nmropt = 1,
ntt = 1, temp0 = 300.0, tempi = 5.0, tautp = 1.0,
ntb = 1,
ntc = 2, ntf = 1,
ioutfm = 1, iwrap = 1,
ntwe = 1000, ntwx = 1, ntpr = 1, ntwr = 5000,
ntr = 1, restraint_wt = 5.00,
restraintmask='!:WAT & !.H=',
icfe = 1, ifsc = 0, clambda = 0.005, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
/
&ewald
/
&wt
type='TEMP0',
istep1 = 0, istep2 = 8000,
value1 = 5.0, value2 = 300.0
/
&wt type = 'END'
/
HEAT1.in
heating
&cntrl
imin = 0, nstlim = 10000, irest = 0, ntx = 1, dt = 0.002,
nmropt = 1,
ntt = 1, temp0 = 300.0, tempi = 5.0, tautp = 1.0,
ntb = 1,
ntc = 2, ntf = 1,
ioutfm = 1, iwrap = 1,
ntwe = 1000, ntwx = 1, ntpr = 1, ntwr = 5000,
ntr = 1, restraint_wt = 5.00,
restraintmask='!:WAT & !.H=',
icfe = 1, ifsc = 0, clambda = 0.005, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
crgmask = ':1.C4,H1,H8,H9,H10'
/
&ewald
/
&wt
type='TEMP0',
istep1 = 0, istep2 = 8000,
value1 = 5.0, value2 = 300.0
/
&wt type = 'END'
/
When I turned off SHAKE (dt=0.001, ntc=1) i saw how isobutane transforms at
n-butane near step 20 and blowing immediately after this event. When
heating at vdw_bonded stage all looks great. Is it "normal" behaviour and
heating when decharging is forbidden action or something wrong with my
system?
All topology and input files provided by the link (archive):
https://drive.google.com/open?id=0B5NzD-LVrUalUzJWMjlsN0djVGM
Thank you,
Artem
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Received on Fri Feb 24 2017 - 08:30:03 PST
