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 Tue Sep 30 2003 - 02:53:01 PDT
