AMBER Archive (2004)

Subject: Re: AMBER: LES question

From: Lishan Yao (yaolisha_at_mail.msu.edu)
Date: Tue Feb 10 2004 - 15:02:18 CST

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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