AMBER Archive (2004)

Subject: Re: AMBER: LES question

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Tue Feb 10 2004 - 15:01:12 CST

Well, to me it seems that you are coupling the LES region to another
bath. My LES protocols run properly now but I am using the same
temperature for both LES non-LES. I guess it would be useful if you give
an input file both from your addles and from your dynamics so people can
judge what's up
vlad

Lishan Yao wrote:

>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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-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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