Dear Prof. Carlos,
Great thanks for your kind help.
Now, when I use rcrd, addles works fine.
But after the completion of addles, it generate the les.top, les.crd, and I
want to use the newly generated parameter file to run minimization with
sander.LES using the following command:
nohup sander.LES -O -i min.in -o min.out -p les.top -c les.crd -r min.restrt&
After the execution of above command, In the command line, I
type"top" and fine sander.LES is in run. However, the size of the file
min.out is zero
even when the sander.LES has run long time.
When I just run 200 steps of sander.LES with a single cpu of 2.5GZ
, after ten minutes, the minimization is still in run . I think it is
abnormal and kill it.
However ,when the sander.LES is killed, the min.out has the following message:
-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 05/15/2006 at 13:53:49
[-O]verwriting output
File Assignments:
| MDIN: min1.in
| MDOUT: min.out
|INPCRD: leshpp.crd
| PARM: leshpp.top
|RESTRT: min.restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
LES minimization
&cntrl
imin = 1,
maxcyc =100,
ncyc = 1000,nsnb=25,
ntr = 0,
ntb = 1,
igb = 0,ntpr=50,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: LES
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info not found in inpcrd
|Largest sphere to fit in unit cell has radius = 0.000
What is the problem?
Best regards
Pang Zhao
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Received on Wed May 17 2006 - 06:07:09 PDT
