-------------------------------------------------------
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.mail.msu.edu>
> To: <amber.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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Received on Wed Feb 11 2004 - 14:53:00 PST
