On Fri, 24 Feb 2017 19:11:53 +0300
Artem Shekhovtsov <job.shekhovtsov.gmail.com> wrote:
> 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.
This is not really such a simple system because you will end up with
both disappearing _and_ appearing atoms (= "create" atoms which will
need to push other atoms aside at some lambda). Ideally you would
avoid this. But you don't really say how you have mapped atoms if
any. You also do not used softcore atoms (ifsc=0) which in such cases
can easily lead to overlaps.
> 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 - 09:00:02 PST
