AMBER Archive (2004)

Subject: AMBER: LES question

From: Lishan Yao (yaolisha_at_mail.msu.edu)
Date: Tue Feb 10 2004 - 14:47:20 CST

Hi:
    I posted this problem about two weeks ago. And I really appreciate
all the responses, which helped me solve several problems. But
sander.LES still can't be run correctly.
    Here is the output I got from sander.LES. 1). The number of water
molecule is wrong. It should be about 15000. 2). The total charge is a
little bit larger than what it should be. I think something is wrong
with topology file. But I exactly follow the manual. And there is no
complaint when I run addles.What could be wrong?

Thanks in advance.

Best,
Lishan

 Number of triangulated 3-point waters found: 7767
| Atom division among processors:
| 0 28277 56555
| Running AMBER/MPI version on 2 nodes

     Sum of charges from parm topology file = 0.00018743
     Forcing neutrality...

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

# degrees of freedom in non-LES region: 116597.
# degrees of freedom in LES region: 0.
 LES particles coupled to separate bath
    LES target temperature: 0.00
    LES target kinetic energy: 0.00
non-LES target temperature: 300.00
non-LES target kinetic energy: 34754.19
 ---------------------------------------------------
 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 = 0.3242E-14 at 2.436720
| CHECK d/dx switch(x): max rel err = 0.8156E-11 at 2.782960
 ---------------------------------------------------

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