AMBER Archive (2004)

Subject: Re: AMBER: LES question

From: Lishan Yao (yaolisha_at_mail.msu.edu)
Date: Thu Jan 29 2004 - 08:46:22 CST

Hi:
   I made a mistake by using the old binary. Now the program doesn't
complain about size issue. But then the program dies immediately after
start. My first question is why # degrees of freedom in LES region
is 0? Then why it dies?

# degrees of freedom in non-LES region: 158528.
# 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: 47252.93
 ---------------------------------------------------
 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
 ---------------------------------------------------

Best,
Lishan

On Wed, 2004-01-28 at 17:28, Carlos Simmerling wrote:
> if you redefined MAXINT and recompiled, does the new
> output list the new MAXINT or the old one? If the old one,
> are you sure you are using the new binary? are you sure
> it was properly recompiled?
>
> ----- Original Message -----
> From: "Lishan Yao" yaolisha_at_mail.msu.edu
> To: <amber_at_scripps.edu>
> Sent: Wednesday, January 28, 2004 5:17 PM
> Subject: Re: AMBER: LES question
>
>
> > Hi:
> > Thanks for your response. Now I'm using sander.LES. But I get this new
> > problem from the output. I changed MAXINT in sizes.h and recompiled it.
> > But the output gives me the same complain.Do I need to change something
> > else?
> >
> > Static Integer Memory requirement of: 8486978 exceeds MAXINT of
> > 8000000
> >
> > Thanks.
> > Lishan
> >
> > On Wed, 2004-01-28 at 14:03, Carlos Simmerling wrote:
> > > ayou should be using sander.LES. if you are already
> > > using that and still get the error, please send a copy of
> > > your script that runs sander.
> > > carlos
> > >
> > > ----- Original Message -----
> > > From: "Lishan Yao" <yaolisha_at_mail.msu.edu>
> > > To: <amber_at_scripps.edu>
> > > Sent: Wednesday, January 28, 2004 1:52 PM
> > > Subject: AMBER: LES question
> > >
> > >
> > > > Dear amber users:
> > > > I try to use LES simulation in amber 7 for my protein ligand
> complex
> > > > system. I get this error. Can anyone tell me which file should I
> change
> > > > to compile?
> > > >
> > > > Thanks in advance.
> > > > Lishan
> > > >
> > > > *** THIS VERSION WILL NOT ACCEPT TOPOLOGY FILES
> > > > THAT WERE CREATED BY ADDLES, WITH NPARM=1
> > > > USE A VERSION COMPILED WITH -DLES
> > > >
> > > >
> > > >
> > >
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