pawan
i also faced this type of problem some time before. i think if u will carry
out a longer NPT run this will be solved .
tell me if any other queery
On 6/19/07, Pavan G <pavanamber.gmail.com> wrote:
>
>
>
> Hello All!
> >
> > Following are the input files I used to study a system of protein
> > surrounded by drugs (parameterized using antechamber).
> >
> > ==============
> > First I minimized the system with restraints on residues 1-420 which
> > were picked from a previous simulation which was stabilized over a few
> > nanoseconds at 312 K. This part (1-420) was picked and surrounded with more
> > water and drugs.
> > ==============
> > minmization
> > &cntrl
> > imin = 1,
> > maxcyc = 5000,
> > ntpr = 100,
> > ncyc = 500,
> > ntr = 1,
> > restraint_wt = 2.0,
> > restraintmask = ':1-420'
> > /
> > ================
> > Then I heated the system from 250K to 400K again with the first 420
> > residues restrained.
> > ==============
> > 500ps heating with NVT
> > &cntrl
> > imin = 0,
> > irest = 0,
> > nstlim = 500000,
> > dt = 0.001,
> > tempi = 250,
> > temp0 = 400,
> > cut = 8,
> > ntb = 1,
> > ntt = 1,
> > ntf = 2,
> > ntc = 2,
> > ntpr = 1000,
> > ntwr = 1000,
> > ntwx = 1000,
> > ntwe = 1000,
> > ntr = 1,
> > restraint_wt = 2.0,
> > restraintmask =':1-420'
> > /
> > =========================
> > Cooling the system to 312K with restraints on first 420 residues
> > =========================
> > 100ps cooling with NVT
> > &cntrl
> > imin = 0,
> > irest = 1,
> > ntx = 5,
> > nstlim = 100000,
> > dt = 0.001,
> > tempi = 402.37,
> > temp0 = 312,
> > cut = 8,
> > ntb = 1,
> > ntt = 1,
> > ntf = 2,
> > ntc = 2,
> > ntpr = 1000,
> > ntwr = 1000,
> > ntwx = 1000,
> > ntwe = 1000,
> > ntr = 1,
> > restraint_wt = 2.0,
> > restraintmask =':1-420'
> > /
> > ==========================
> > NPT at 312K on the whole system. No restraints on any part of the system
> >
> > ==========================
> > 200ps NPT
> > &cntrl
> > imin = 0,
> > irest = 1,
> > ntx = 5,
> > nstlim = 200000,
> > dt = 0.001,
> > tempi = 312,
> > temp0 = 312,
> > cut = 8,
> > ntb = 2,
> > ntp = 1,
> > taup = 2.0,
> > ntt = 1,
> > ntf = 2,
> > ntc = 2,
> > tautp = 1,
> > ntpr = 1000,
> > ntwr = 1000,
> > ntwx = 1000,
> > ntwe = 1000,
> > /
> > ==========================
> >
> > All the plots, temperature, Etot, etc. don't have any major
> > fluctuations. The Ewald error estimate for NPT had a mean of 5*10^(-5) and a
> > standard deviation of 3*10(-5). Should this be a cause for alarm?
> > When I imaged the frames to center the initial 420 residues I ended up
> > with a system which was fine when looked at two planes (rectangular).
> > However when viewed it along the third plane, it looked like a plus symbol.
> > (Figure attached).
> > Could you please comment on why it turned out that way. I don't see a
> > reason why it should have the edges filletted and even if should, why only
> > in one direction?
> > Please let me know if you want any additional information.
> >
> > Thank you,
> > Pavan K. Ghatty
> >
> >
>
>
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Received on Sun Jun 24 2007 - 06:07:03 PDT
