On 9/3/2012 8:40 PM, Subrata Paul wrote:
> Dear Amber User's,
>
> I have carried out a MD simulation with following input file..
> *md.in*
> &cntrl
> imin=0,
> irest=1,
> ntx=7,
> ntb=2,
> ntp=1,
> scee=1.2,scnb=2.0,
> iwrap=1,
> pres0=1.0,
> taup=2.0,
> ntc=2, ntf=2,
> ntt=3, gamma_ln=1.0,
> temp0=300.0,
> ntpr=2000, ntwx=2000,
> nstlim=250000,
> dt=0.002,
> cut=10.0
> /
>
> Here, some extra line is coming in the out put file like ''wrapping first
> mol''
>
>
> NSTEP = 204000 TIME(PS) = 5438.000 TEMP(K) = 303.55 PRESS =
> -82.3
> Etot = -2429.1029 EKtot = 2836.5846 EPtot =
> -5265.6875
> BOND = 265.6921 ANGLE = 680.5595 DIHED =
> 3077.2740
> 1-4 NB = 234.0765 1-4 EEL = 9799.2699 VDWAALS =
> 1278.0487
> EELEC = -20600.6082 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 969.7679 VIRIAL = 1042.8679 VOLUME =
> 41161.3393
> Density =
> 1.1310
> Ewald error estimate: 0.1312E-03
> ------------------------------------------------------------------------------
>
> wrapping first mol.: 34.51532 0.00000 0.00000
> wrapping first mol.: 34.52674 0.00000 0.00000
> wrapping first mol.: 34.53183 0.00000 0.00000
> wrapping first mol.: 34.52109 0.00000 0.00000
> wrapping first mol.: 34.52109 0.00000 0.00000
>
>
> Why this wrapping first mol is written in the out put file?
> is this a error?
>
>
Are you writing to mdcrd? Can you watch the movie and see if the first
molecule is being translated across the box?
Bill
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Received on Mon Sep 03 2012 - 21:30:02 PDT
