Hello Adrian,
You guessed it right. I am interested in the diffusion constants in the
system which is the reason why I did not use iwrap=1 and later used ptraj
for processing the output.
Pavan
On 6/19/07, Adrian Roitberg <roitberg.qtp.ufl.edu> wrote:
>
> Pavan,
> First guess is that you need to center/image your MD run (using ptraj).
> It is always wise to use iwrap=1 in your md runs, unless you are really
> interested in diffusion properties.
>
> Adrian
>
>
> Pavan G 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
> >>
> >>
> >
> >
> > ------------------------------------------------------------------------
> >
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project and Department of Chemistry
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
>
> ============================================================================
>
> To announce that there must be no criticism of the president,
> or that we are to stand by the president right or wrong,
> is not only unpatriotic and servile, but is morally treasonable
> to the American public."
> -- Theodore Roosevelt
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jun 20 2007 - 06:07:36 PDT
