can you forward to me (not the whole list) the
complete output file? I need to see how your
temperature coupling is defined and what the error
message is.
----- Original Message -----
From: "Lishan Yao" <yaolisha.mail.msu.edu>
To: <amber.scripps.edu>
Sent: Thursday, January 29, 2004 9:46 AM
Subject: Re: AMBER: LES question
> 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.mail.msu.edu
> > To: <amber.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.mail.msu.edu>
> > > > To: <amber.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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Received on Fri Jan 30 2004 - 18:56:04 PST
