Dear Sir,
yes, I am writing the mdcrd file.
The first molecule try to escape from the cubic box , but it can not.
Since, iwrap=1 is used in the input file.
is this a error ?
On Tue, Sep 4, 2012 at 9:57 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> 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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--
*With Best Regards
Subrata
PhD Student
Dept of Chemistry.
IIT G
*
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Received on Mon Sep 03 2012 - 22:00:02 PDT
