AMBER Archive (2003)

Subject: Re: Re: AMBER: nstlim

From: uddhavesh bhaskar sonavane (ubs3_at_rediffmail.com)
Date: Wed Oct 01 2003 - 10:32:27 CDT

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_at_scripps.edu> >To: <amber_at_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_at_scripps.edu > > To: owner-amber_at_scripps.edu > > Subject: BOUNCE amber_at_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 > > > > > > ___________________________________________________ > > Meet your old school or college friends from > > 1 Million + database... > > Click here to reunite www.batchmates.com/rediff.asp > > > > > > > > > > ----------------------------------------------------------------------- > > The AMBER Mail Reflector > > To post, send mail to amber_at_scripps.edu > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu > > > > > > > >----------------------------------------------------------------------- >The AMBER Mail Reflector >To post, send mail to amber_at_scripps.edu >To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu >

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