AMBER Archive (2009)

Subject: Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Mar 31 2009 - 21:24:34 CDT

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_at_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_at_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_at_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_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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> >
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