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 - 13:37:18 CDT

Hello Ross,

You're right. My system's initial density was too low since I had used tleap
to surround the protein with boxes of (water+drug) which left pretty large
sized gaps and yes the NVT was rather long. But I was under the impression
that all instabilities in density will be taken care of once I start NPT. I
am currently following the protocol you suggested. Will keep you posted on
the status.

Thanks for the informative mail.
Pavan K. Ghatty

On 6/19/07, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> Dear Pavan,
>
> The image you show is indicative of having vacuum bubbles present in your
> simulation. You can see this clearly if you open the trajectory or restrt
> file in VMD and then under graphical representations select periodic and
> turn on the periodic images. Then you will see the bubbles crossing the edge
> of the box.
>
> This occurs because the initial density of the system is too low -
> required for stability initially. You then run with NVT for too long and the
> system forms these vacuum bubbles that can take an extremely long time to
> equilibrate out.
>
> I suggest you try the following protocol:
>
> 1) Minimize
>
> 2) NVT 0 to 100K (20ps or so)
>
> 3) NPT 100 to 300K (100ps or so) - density should equilibrate around 1.
>
> 4) Continue with NPT, NVT or NVE, your choice.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> ------------------------------
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Pavan G
> *Sent:* Tuesday, June 19, 2007 07:35
> *To:* amber_at_scripps.edu
> *Subject:* Re: AMBER: Re: Strange shape in my MD simulations
>
> 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
> > >> To post, send mail to amber_at_scripps.edu
> > >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >>
> > >
> >
> > --
> > 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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