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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Received on Wed Apr 01 2009 - 01:18:48 PDT
