Dear Sir
The fllowing result is sourcing from the parameters of locmem.f changed .
minimazation:
&cntrl
imin = 1,
maxcyc = 500,
ncyc = 250,
ntb = 1,
igb = 0,
ntr = 0,
cut = 8
/
errors:
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
---------------------------------------------------
* NB pairs 1385 6666506 exceeds capacity ( 6666666)
SIZE OF NONBOND LIST = 6666666
SANDER BOMB in subroutine nonbond_list
Non bond list overflow!
check MAXPR in locmem.f
2011-06-13
hanlu0366
发件人： David A. Case
发送时间： 2011-06-11 22:03:42
收件人： AMBER Mailing List
抄送：
主题： Re: [AMBER] problems ahout simulating a molecular crystal
On Fri, Jun 10, 2011, hanlu0366 wrote:
> I am sure that my sander is '~/amber11/bin/sander ' . The same errors
> happen when the value of cut changed is 8.
>
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
> ---------------------------------------------------
>
> * NB pairs 1385 6666506 exceeds capacity ( 6666666)
> SIZE OF NONBOND LIST = 6666666
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
OK: you crystal is probably slightly denser than typical biomolecules, and the
estimate of the amount of space for the nonbonded list must be too small.
In locmem.f, find these lines:
! --- crude (but useful?) estimate for MAXPR:
! DAN ROE: Does this need to be changed for hybridgb
if( igb /= 0 .or. ipb /= 0 ) then
maxpr = 1
else
if( numextra == 0 ) then
maxpr_float = natom * (cutoffnb + skinnb)**3 / 3.0d0 <====
else ! need more nonbon storage with extra points
maxpr_float = natom * (cutoffnb + skinnb)**3 / 2.5d0
end if
and change the "3.0d0" by the arrow above to 2.d0. You should continue to use
a value in the range of 8-10 for "cut".
...good luck...dac
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Received on Mon Jun 13 2011 - 06:30:03 PDT
