AMBER Archive (2004)

Subject: Re: AMBER: LES question

From: xiaolin cheng (cheng_at_ilion.bio.sunysb.edu)
Date: Tue Feb 10 2004 - 18:14:31 CST

It seems to me that you are trying to run a simulation from a restart file.
But your input coordinate file ycd_1p60_les.inpcrd only contains
coordinates.
try ntx =1, irest = 0 instead.

xiaolin
----- Original Message -----
From: "Lishan Yao" <yaolisha_at_mail.msu.edu>
To: <amber_at_scripps.edu>
Sent: Tuesday, February 10, 2004 4:02 PM
Subject: Re: AMBER: LES question

> Hi:
> Here are input files for two programs.
>
> Input file for addles.
>
> file rprm name=(ycd_1p60_new.prmtop) read
> file rcvb name=(md_npt1.restrt) read
> file wprm name=(ycd_1p60_les.prmtop) wovr
> file wcrd name=(ycd_1p60_les.inpcrd) wovr
> action
> omas
> spac numc=4 pick #mono 107 115 done
> spac numc=4 pick #mono 146 156 done
> spac numc=4 pick #mono 268 276 done
> spac numc=4 pick #mono 307 317 done
> *EOD
>
>
> Input file for sander.LES
>
> molecular dynamics run
> &cntrl
> imin=0,irest=1,ntx=5,tempi=100.0,
> ntt=1,temp0=300.0,tautp=0.5,
> ntp=0,
> ntb=1,ntc=2,ntf=2,
> nstlim=250000,dt=0.002,
> ntwe=1000,ntwx=1000,ntpr=100,
> &end
>
>
> Lishan
>
>
>
> Tue, 2004-02-10 at 16:01, Vlad Cojocaru wrote:
> > 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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> > >
>
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