Hello
I have a quick amber question.
Ever since you help me solve my issue of nonbond list,
i have ran some of my test jobs successfully.
However i have this question about the .out file of an
equilibration run on my molecules.
NMR restraints: Bond = 0.000 Angle = 0.000
Torsion = 0.000
===============================================================================
check COM velocity, temp: 0.000000
0.00(Removed)
NSTEP = 39000 TIME(PS) = 178.000 TEMP(K) =
299.20 PRESS = 81.4
Etot = -147615.0619 EKtot = 48990.7857
EPtot = -196605.8476
BOND = 4956.2820 ANGLE = 12370.4467
DIHED = 13171.6740
1-4 NB = 7241.3883 1-4 EEL = 71238.2113
VDWAALS = 14375.7827
EELEC = -319959.6327 EHBOND = 0.0000
RESTRAINT = 0.0000
EKCMT = 16618.7403 VIRIAL = 15280.0158
VOLUME = 761548.1213
Density = 1.0575
Ewald error estimate: 0.1094E-04
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000
Torsion = 0.000
===============================================================================
-The simulation seems to be stuck at that point.
However it has not crashed on me yet, and has not
changed for the past 24 hours. so i was wondering
whether it is a very big problem or just a matter of
the number of atom (21000).
Below is my sander command line and input file
sander -O -i shortmd.in -o rldhequil.out -c
rldhminanneal.rst -p rldh_sol.top -r rldhequil.rst
Dynamic Simulation with Constant Volume
# Control section
&cntrl
ntwx = 500, ntpr = 500, ntwr = 500,
ntt = 1, temp0 = 300.0, tempi = 17.0, tautp = 1.0,
scnb = 1.0, scee = 1.0, dielc = 1, cut = 8.0,
ntb = 2, ntc = 2, ntf = 2,
nstlim = 75000, dt = 0.0020,
ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,
ibelly = 0, ntr = 0, iwrap=1,
imin = 0, irest = 0, ntx = 1, nmropt = 1,
&end
&ewald
skinnb = 1.0,
nbflag = 1,
&end
&wt
type = 'TEMP0', istep1 = 1, istep2 = 35000, value1 =
17.0, value2 = 300.0,
&end
&wt
type = 'TEMP0', istep1 = 35001, istep2 = 75000,
value1 = 300.0, value2 = 300.0,
&end
&wt
type='END'
&end
&rst IAT(1) = 0 &end
END
Thanks for your help and cooperation
Neville
-- "David A. Case" <case.scripps.edu> wrote:
> On Mon, Jul 02, 2007, Dan Kidger wrote:
> >
> > Both Amber8 and Amber9 contain the line
> > nogrdptrs=nogrdptrs .or.( (nucgrd1 <=
> 2*nghb+2) .or. &
> > (nucgrd1 <= 2*nghb+2) .or. &
> > (nucgrd1 <= 2*nghb+2) )
> > in subroutine setup_grids()
> >
> > This looks wrong since all three of the
> conditioned or-ed together are
> > identical
>
> Thanks for the report. At least part of this is now
> incorporated into
> bugfix.36.
>
> ...regards...dac
>
>
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Received on Sun Aug 12 2007 - 06:07:17 PDT
