Set dt to > 0.0000 - I am betting that gives you a divide by zero
somewhere.
On 2/18/14, 9:42 PM, "kurisaki" <kurisaki.ncube.human.nagoya-u.ac.jp>
wrote:
>Dear Amber developers and users,
>
>I performed 1-step MD simulation
>To calculate pressure from a resterat file.
>
>The pressure value is written as expected,
>But temerature, and also kinetic values, are shown as NaN, not calculated.
>
>Does the pressure value neglect the term of temperature?
>
>
>>>>
>NSTEP = 1 TIME(PS) = 5151.000 TEMP(K) = NaN PRESS =
>214.2
> Etot = NaN EKtot = NaN EPtot =
>-60985.1928
> BOND = 298.7552 ANGLE = 807.3912 DIHED =
>1066.4506
> 1-4 NB = 373.2392 1-4 EEL = 4480.6187 VDWAALS =
>7679.7242
> EELEC = -75691.3719 EHBOND = 0.0000 RESTRAINT =
>0.0000
> EKCMT = 5440.3586 VIRIAL = 4525.7050 VOLUME =
>197734.6841
> Density =
>1.0100
> Ewald error estimate: 0.9795E-04
>
>--------------------------------------------------------------------------
>----
><<<
>
>
>To run pmemd, I used the following the mdin file.
>
>>>>
>
>Molecular Dynamics
>
> &cntrl
>
> TIMLIM = 999999, IMIN = 0,
>
>
>
> NTX = 5, IREST = 1, NTRX = 1,
>
>
>
> NTXO = 1, NTPR = 0, NTWR = 0, IWRAP = 0,
>
> NTWX = 500, NTWV = 0,
>
>
>
> NTF = 2, NTB = 2,
>
> CUT = 9.0,
>
>
>
> NSTLIM = 0, NSCM = 500,
>
> T = 0.0000, DT = 0.00000,
>
>
>
> NTT = 0,
>
>
>
> NTP = 1, PRES0 = 1.000, COMP = 44.600, TAUP = 2.000,
>
>
>
> NTC = 2, TOL = 0.000001,
>
>
>
>/
><<<<
>
>
>I am most grateful if you give me some advises or comments.
>
>Yours sincerely,
>
> Ikuo KURISAKI
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 18 2014 - 22:00:05 PST
