Last week I came across the following papers:
M. A. Balsera, W. Wriggers, Y. Oono, and K. Schulten, “Principal Component
Analysis and Long Time Protein Dynamics”, J. Phys. Chem. 1996, 100,
2567-2572.
L. S. Caves, J. D. Evanseck, and M. Karplus, “Locally accessible
conformations of proteins: Multiple molecular dynamics simulations of
crambin”,* *Protein Science* *(1998), 7649-666.
In the last paper (which is old) they advocate using multiple short
simulations with new velocity assigments. I think the only way to do this in
AMBER is by setting ntx=0, irest=1, and ig=-1 otherwise the same velocities
will be assigned for all simulations. Some results have interesting features
and I was wondering what seeds were used, and hence what initial velocities
were being assigned.
On Tue, Mar 31, 2009 at 10:24 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I don't think any of this is relevant since you have ntt=0 and therefore no
> thermostat. is that what you really want?
>
> On Tue, Mar 31, 2009 at 10:15 PM, Naser Alijabbari <na3m.virginia.edu
> >wrote:
>
> > I am using Amber 10 and these are the parameters for a test run in
> sander.
> >
> > &cntrl
> > imin = 0, irest = 0, ntx = 1,
> > ntb = 1,
> > cut = 10, ntr = 0,
> > ntc = 2, ntf = 2, tol=.000001,
> > tempi = 300, temp0 = 300.0, ig=-1,
> > ntt = 0, nscm=0,
> > nstlim = 95000, dt = 0.001,
> > ntpr = 100, ntwx = 50, ntwr = 1000,
> > &end
> > &ewald
> >
> > ew_type=0,
> > dsum_tol=0.00001,
> > &end
> >
> > END
> >
> >
> > I am not sure where ig comes into setvel. In mdread there is only 'if(
> > ig==-1 ) call microsec(ig)'
> >
> > ! Assign velocities from a Maxwellian distribution.
> >
> > subroutine setvel(nr,v,winv,tempi,init,iscale,scalm)
> >
> > use amoeba_mdin, only : iamoeba,beeman_integrator
> >
> > implicit none
> >
> >
> >
> > double precision v(*),winv(*),tempi,scalm
> >
> > integer nr,init,iscale
> >
> >
> >
> > integer i,j,nr3, icopy
> >
> > double precision boltz,sd
> >
> >
> >
> > nr3 = 3*nr
> >
> >
> >
> > ! ----- Assign velocities from a Maxwellian distribution
> >
> >
> >
> > if (tempi < 1.d-6) then
> >
> > v(1:nr3+iscale) = 0.d0
> >
> > return
> >
> > end if
> >
> >
> >
> > boltz = 8.31441d-3*tempi/4.184d0
> >
> > i = 0
> >
> > do j=1,nr
> >
> > sd = sqrt(boltz*winv(j))
> >
> > call gauss(0.d0,sd,v(i+1))
> >
> > call gauss(0.d0,sd,v(i+2))
> >
> > call gauss(0.d0,sd,v(i+3))
> >
> > i = i+3
> >
> > end do
> >
> > if (iscale > 0) then
> >
> > sd = sqrt(boltz/scalm)
> >
> > do j=1,iscale
> >
> > call gauss(0.d0,sd,v(i+j))
> >
> > end do
> >
> > end if
> >
> > if ( iamoeba == 1 .and. beeman_integrator == 1 )then
> >
> > do j=1,nr3
> >
> > v(j) = 20.455d0*v(j) ! beeman uses time in ps units
> >
> > enddo
> >
> > endif
> >
> > return
> >
> > end subroutine setvel
> >
> > On Tue, Mar 31, 2009 at 9:41 PM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > in dynlib.f:
> > >
> > > ! Assign velocities from a Maxwellian distribution.
> > > subroutine setvel(nr,v,winv,tempi,init,iscale,scalm)
> > >
> > > look in mdread.f- ig should be written to the mdout file for ntt=2 or
> 3.
> > >
> > > this assumes amber10, so you'll need to be more specific if this
> doesn't
> > > solve your problem.
> > >
> > >
> > > On Tue, Mar 31, 2009 at 9:35 PM, Naser Alijabbari <na3m.virginia.edu>
> > > wrote:
> > >
> > > > The default value for ig=71277, but is there a way to find what was
> > used
> > > as
> > > > a seed when ig=-1?
> > > > Also where is the routine for assigning velocities
> > > > according Maxwell-Boltzmann distribution? fgrep of the sander source
> > code
> > > > only returns poisson_boltzmann routine.
> > > > Naser
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
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> > >
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> >
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Received on Wed Apr 01 2009 - 01:18:55 PDT
