Re: Re: AMBER: nstlim

From: Robert Duke <rduke.email.unc.edu>
Date: Wed, 1 Oct 2003 12:32:48 -0400

Uddhavesh -
Also not a problem, out to the limits of 4 byte integer arithmetic, or 2,147,483,647. I wouldn't try more than that ;-). I know the print format overflow is annoying. I will bump up the fields in pmemd 3.1.
Regards - Bob Duke
  ----- Original Message -----
  From: uddhavesh bhaskar sonavane
  To: amber.scripps.edu
  Sent: Wednesday, October 01, 2003 11:32 AM
  Subject: Re: Re: AMBER: nstlim


  Hello Sir,
            The NSTEP Format is also overflowing (See attached o/p). Will it affect analysis part. Kindly, let me just know what are the consequences of this thing.

  NSTEP =995000 TIME(PS) = 2530.000 TEMP(K) = 300.66 PRESS = 25.35
  Etot = -109448.4709 EKtot = 25518.1918 EPtot = -134966.6627
  BOND = 113.6654 ANGLE = 307.1367 DIHED = 327.6174
  1-4 NB = 132.7118 1-4 EEL = 1848.3488 VDWAALS = 19750.0857
  EELEC = -157446.2285 EHBOND = 0.0000 CONSTRAINT = 0.0000
  EKCMT = 12533.3597 VIRIAL = 12297.8966 VOLUME = 430172.7828
                                                  Density = 0.9891
  Ewald error estimate: 0.8056E-04
  ------------------------------------------------------------------------------

  check COM velocity, temp: 0.000000 0.00(Removed)

  NSTEP =****** TIME(PS) = 2540.000 TEMP(K) = 297.75 PRESS = 62.58
  Etot = -109503.9425 EKtot = 25271.2384 EPtot = -134775.1809
  BOND = 114.2998 ANGLE = 304.8698 DIHED = 320.4762
  1-4 NB = 125.3418 1-4 EEL = 1838.4879 VDWAALS = 19712.7356
  EELEC = -157191.3920 EHBOND = 0.0000 CONSTRAINT = 0.0000
  EKCMT = 12406.9753 VIRIAL = 11826.3181 VOLUME = 429737.1214
                                                  Density = 0.9901
  Ewald error estimate: 0.4585E-04
  ------------------------------------------------------------------------------


  Waiting for reply,

  Uddhav

    


  On Tue, 30 Sep 2003 Robert Duke wrote :
>Uddhav -
>This is not a problem. The nstlim field is just in the Sander 6 format, and
>the output overflows, I would guess at values over 99,999. The internal
>value is whatever you specified in the mdin, which is part of the preceding
>output. Also, the nstep field is i7, so you can do step counting out to
>9,999,999 steps. More annoying than this is the overflow of some of the
>energy fields in the amber 6 format for larger systems - around 200,000
>atoms or more. I am working on the 3.1 release of pmemd, and may open up
>the formats on some of this stuff, just to cut down on the annoyance.
>Regards - Bob
>
>----- Original Message -----
> From: "Amber Administration" <amber-admin.scripps.edu>
>To: <amber.scripps.edu>
>Sent: Monday, September 29, 2003 7:55 PM
>Subject: AMBER: nstlim
>
>
> > Hello,
> >
> > This message triggered our spam filters which have been relaxed.
> >
> > Amber Admin
> >
> > ---------- Forwarded message ----------
> > Date: Fri, 26 Sep 2003 03:22:42 -0700 (PDT)
> > From: owner-amber.scripps.edu
> > To: owner-amber.scripps.edu
> > Subject: BOUNCE amber.scripps.edu: taboo body match "/Click here/" at
> > line 69
> >
> > Hello,
> > I am running MD simulation for 1 ns using pmemd 3.03.
> > Although simulation is going on, its has not writting NSTLIM
> > value. Its showing in o/p file as NSTLIM=*****
> > That part of o/p is attached below. Kindly suggest
> > Whether the simulation will go for long time or it will terminate
> > after 1 ns.
> >
> > Uddhav
> >
> >
> > O/p part:
> >
> > TIMLIM= 999999. IREST = 1 IBELLY= 0
> > IMIN = 0
> > IPOL = 0
> >
> > NTX = 7 NTXO = 1
> > IG = 71277 TEMPI = 300.00 HEAT = 0.000
> >
> > NTB = 2 BOXX = 82.379
> > BOXY = 82.379 BOXZ = 82.379
> >
> > NTT = 1 TEMP0 = 300.000
> > DTEMP = 0.000 TAUTP = 0.500
> > VLIMIT= 20.000
> >
> > NTP = 1 PRES0 = 1.000 COMP = 44.600
> > TAUP = 0.200 NPSCAL= 1
> >
> > NTCM = 0 NSCM = 1000000
> >
> > NSTLIM=***** NTU = 1
> > T = 0.000 DT = 0.00200
> >
> > NTC = 2 TOL = 0.00000 JFASTW = 0
> >
> > NTF = 2 NSNB = 10
> >
> > CUT = 9.000 SCNB = 2.000
> > SCEE = 1.200 DIELC = 1.000
> >
> > NTPR = 5000 NTWR = 5000 NTWX = 5000
> > NTWV = 0 NTWE = 0 IOUTFM= 0
> > NTWPRT= 0 NTWPR0= 0 NTAVE= 0
> >
> > NTR = 0 NTRX = 1
> > TAUR = 0.00000 NMROPT= 0 PENCUT= 0.10000
> >
> > IVCAP = 0 MATCAP= 0 FCAP = 1.500
> >
> > OTHER DATA:
> >
> > IFCAP = 0 NATCAP= 0 CUTCAP= 0.000
> > XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000
> >
> > VRAND= 0
> >
> > NATOM = 42563 NRES = 14025
> >
> > Water definition for fast triangulated model:
> > Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ;
> > Hyd2_name = H2
> >
> >
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Received on Wed Oct 01 2003 - 17:53:02 PDT
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