AMBER Archive (2009)

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

From: Naser Alijabbari (na3m_at_virginia.edu)
Date: Tue Mar 31 2009 - 21:15:13 CDT

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
> >
> _______________________________________________
> AMBER mailing list
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