AMBER Archive (2004)

Subject: Re: AMBER: LES question

From: Lishan Yao (yaolisha_at_mail.msu.edu)
Date: Wed Feb 11 2004 - 08:16:01 CST

          -------------------------------------------------------
          Amber 7 SANDER Scripps/UCSF 2002
          -------------------------------------------------------

| Mon Feb 9 17:10:41 2004

  [-O]verwriting output

File Assignments:
| MDIN: md_nvt1.in
| MDOUT: md_nvt1.out
|INPCRD: ycd_1p60_les.inpcrd
| PARM: ycd_1p60_les.prmtop
|RESTRT: md_nvt1.restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: md_nvt1.ene
| MDCRD: md_nvt1.crd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 Here is the input file:

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

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags: MPI LES
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
 NATOM = 56555 NTYPES = 31 NBONH = 53068 MBONA = 3563
 NTHETH = 7602 MTHETA = 4807 NPHIH = 13805 MPHIA = 8419
 NHPARM = 0 NPARM = 1 NNB = 731136 NRES = 16912
 NBONA = 3563 NTHETA = 4807 NPHIA = 8419 NUMBND = 91
 NUMANG = 189 NPTRA = 64 NATYP = 43 NPHB = 1
 IFBOX = 1 NMXRS = 96 IFCAP = 0 NEXTRA = 0

| Memory Use Allocated Used
| Real 8000000 3897600
| Hollerith 1600000 356244
| Integer 16000000 9766881

| Max Nonbonded Pairs:21600000
 LES parameters were found
  194008 LES atom pairs require adjustment
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

General flags:
     imin = 0, nmropt = 0

Nature and format of input:
     ntx = 5, irest = 1, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 100, ntrx = 1, ntwr
= 500
     iwrap = 0, ntwx = 1000, ntwv = 0, ntwe
= 1000
     ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0

Potential function:
     ntf = 2, ntb = 1, igb = 0, nsnb
= 25
     ipol = 0, gbsa = 0
     dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Molecular dynamics:
     nstlim = 250000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00200, vlimit = 20.00000

Temperature regulation:
     ig = 71277, ntt = 1, vrand = 0
     temp0 = 300.00000, tempi = 100.00000, heat = 0.00000
     temp0LES = -1.00000
     dtemp = 5.00000, tautp = 0.50000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
     vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc
= 1
     Box X = 88.612 Box Y = 87.660 Box Z = 71.053
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 90 NFFT2 = 90 NFFT3 = 72
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4
| PLEVEL = 1: runmd parallelization, no EKCMR

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

 begin time read from input coords = 22.500 ps

 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

Lishan

On Wed, 2004-02-11 at 08:48, Carlos Simmerling wrote:
> I don't understand why your sander.LES input says
> you want to use a single temperature bath but
> your output says it is using 2 baths.
> can you send the top of the output file all the way to
> where it lists the # degrees of freedom for LES and
> non-LES regions?
>
> something seems to have gone wrong that I have not
> encountered before. I looked at the code for
> reading user input for 1 vs 2 temperature baths
> and it looks ok.
>
> carlos
>
> ----- 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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