AMBER Archive (2005)

Subject: AMBER: Extended bonds-MD

From: Ananda Rama Krishnan Selvaraj (ananda.selvaraj_at_chemie.uni-halle.de)
Date: Wed Jun 15 2005 - 02:02:25 CDT

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 |
>
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