AMBER Archive (2007)

Subject: Re: AMBER: Re: Strange shape in my MD simulations

From: Pavan G (pavanamber_at_gmail.com)
Date: Tue Jun 19 2007 - 09:34:45 CDT

Yeah, the picture attached is what I got after imaging the protein to the
center of the box. My ptraj input was

trajin mdcrd
image familiar
center :1-420
trajout reimg.mdcrd

Pavan

On 6/19/07, Adrian Roitberg <roitberg_at_qtp.ufl.edu> wrote:
>
> ok, but then use ptraj to center/image before looking at the pictures in
> vmd.
>
> a.
>
>
> Pavan G wrote:
> > 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_at_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_at_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
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> >>
> >
>
> --
> 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_at_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_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

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