AMBER Archive (2005)

Subject: Re: AMBER: Extended bonds-MD

From: Ananda Rama Krishnan Selvaraj (ananda.selvaraj_at_chemie.uni-halle.de)
Date: Wed Jun 15 2005 - 07:55:41 CDT

Dear Prof.Carlos,
              Many thanks..anand

----- Original Message -----
From: Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>
Date: Wednesday, June 15, 2005 1:22 pm
Subject: Re: AMBER: Extended bonds-MD

> It sounds like it might be a problem with the file format in
> the visualization. What program are you using? Are you telling
> it that you have a periodic system? (crdbox in vmd; amber PBC in
> moil-view, etc)
>
> Ananda Rama Krishnan Selvaraj wrote:
>
> >Dear Ross,
> > As per you suggestion, i have changed the input
> parameter for
> >the MD simulation in periodic boundary condition. but again i am
> getting>that extended lines (extended bonds and totally deformed
> structures).>here is the input
> >
> > PIB
>
> >
> >
> >General flags:
> > imin = 0, nmropt = 0
> >
> >Nature and format of input:
> > ntx = 1, irest = 0, ntrx = 1
> >
> >Nature and format of output:
> > ntxo = 1, ntpr = 200, ntrx = 1, ntwr
> =
> > 500
> > iwrap = 0, ntwx = 200, ntwv = 0, ntwe
> =
> > 0
> > ioutfm = 0, ntwprt = 0, idecomp = 0,
> rbornstat=> 0
> >
> >Potential function:
> > ntf = 2, ntb = 1, igb = 0, nsnb
> =
> > 25
> > ipol = 0, gbsa = 0
> > dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
> > scnb = 2.00000, scee = 1.20000
> >
> >Frozen or restrained atoms:
> > ibelly = 0, ntr = 1
> >
> >Molecular dynamics:
> > nstlim = 100000, nscm = 1000, nrespa = 1
> > t = 0.00000, dt = 0.00050, vlimit = 20.00000
> >
> >Temperature regulation:
> > ig = 71277, ntt = 1, vrand = 0
> > temp0 = 10.00000, tempi = 0.00000, heat = 0.00000
> > dtemp = 5.00000, tautp = 1.00000
> >
> >SHAKE:
> > ntc = 2, jfastw = 0
> > tol = 0.00001
> >
> >Ewald parameters:
> > verbose = 0, ew_type = 0, nbflag = 0,
> use_pme =
> > 1
> > vdwmeth = 1, eedmeth = 1, frc_int = 0,
> netfrc =
> > 1
> > Box X = 180.000 Box Y = 40.000 Box Z = 20.000
> > Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> > NFFT1 = 180 NFFT2 = 40 NFFT3 = 20
> > Cutoff= 8.000 Tol =0.100E-04
> > Ewald Coefficient = 0.34864
> > Interpolation order = 4
> >
> >The MD simulation was completed without any error message.
> >Interestingly, every 102 steps (snop shots), i have observed good
> >struture (comparatively, only one C-H bond is extended , other
> bonds are
> >o.k).
> >
> >so could you tell the right way to correct error.
> >
> >
> >moreover, i have started the simulation from the energy minimized
> >structure ( it is o.k.)
> >
> >thanks....anand
> >
> >
> >
> >
> >
> >----- Original Message -----
> >From: Ross Walker <ross_at_rosswalker.co.uk>
> >Date: Tuesday, June 14, 2005 7:28 pm
> >Subject: RE: AMBER: Extended bonds-MD
> >
> >
> >
> >>Dear Ananda
> >>
> >>A few comments on your input options:
> >>
> >>
> >>
> >>>MD_simulation of IMB in PBC_1
> >>> &cntrl
> >>> imin = 0, irest = 0, ntx = 1,
> >>> ntt = 1, temp0 = 10.0,
> >>>
> >>>
> >>temp0=10.0 you only want a temperature of 10 kelvin correct?
> >>
> >>
> >>
> >>>tautp = 1, gamma_ln = 10000,
> >>>
> >>>
> >>gamma_ln is not used when ntt=1 only with ntt=3. For the record
> >>though a
> >>value of 10000 for gamma_ln is huge. A value of 4 or 5 would be more
> >>appropriate.
> >>
> >>
> >>
> >>> ntp = 0,
> >>> ntb = 1, ntc = 1, ntf = 7,
> >>>
> >>>
> >>ntf=7 -> This almost certainly the cause of your problems. This
> >>means omit
> >>all bond angle and dihedral interactions. Do you really want to
> do
> >>this? In
> >>my experience running a simulation of a protein with just non-bonded
> >>interactions is never stable. The only time I find you can get
> away
> >>withNTF>1 is for NTF=2 and only then when you have shake turned
> on
> >>(ntc=2).Also, since you are running a 0.5fs time step there is
> >>nothing to really be
> >>gained from ommiting bonds angles and dihedrals. I would treat
> ntf
> >>valuesgreater than 2 as being developer/debugging options.
> >>
> >>
> >>
> >>> cut = 20.0,
> >>>
> >>>
> >>20 angstroms is probably much much bigger than you need for a
> periodic>>boundary simulation. Set it to 8 angstroms and only
> increase it if
> >>you don't
> >>run with PME.
> >>
> >>
> >>
> >>>scee = 4.0, scnb = 20.0,
> >>>
> >>>
> >>Why have you changed these? These really are developer options
> and
> >>should"never?" be changed by the end user without good reason.
> The
> >>entire force
> >>field (FF99, FF03...) is parameterised around the default values
> of
> >>thesescaling factors. SCNB should be 2.0 and scee should be 1.2.
> >>Only change them
> >>if you have for some reason built yourself a completely new force
> >>field.
> >>
> >>
> >>>keep PIB fixed with strong constraints
> >>>100
> >>>RES 1 64
> >>>END
> >>>END
> >>>
> >>>
> >>100.0 KCal/mol is a pretty big restraint and may cause
> instability
> >>in your
> >>system. It is probably ok for minimisation but I would reduce
> this
> >>duringmolecular dynamics. A value of 10 or less should be
> >>sufficient to keep these
> >>residues fixed reasonably close to the initial structure.
> >>
> >>
> >>
> >>
> >>>is it due to the less simulation time period or the effect of
> box
> >>>
> >>>
> >>size> or the effect of some other parameters.
> >>
> >>This is an artifact of the various "strange" options in your
> input
> >>file that
> >>I have highlighted above.
> >>
> >>All the best
> >>Ross
> >>
> >>/\
> >>\/
> >>|\oss Walker
> >>
> >>| Department of Molecular Biology TPC15 |
> >>| The Scripps Research Institute |
> >>| Tel:- +1 858 784 8889 | 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.
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> >>
> >>
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>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> Stony Brook University Web:
> http://comp.chem.sunysb.edu/carlosStony Brook, NY 11794-5115 E-
> mail: carlos.simmerling_at_stonybrook.edu
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