AMBER Archive (2009)

Subject: Re: [AMBER] the output files

From: oguz gurbulak (gurbulakoguz_at_gmail.com)
Date: Mon Feb 09 2009 - 07:03:47 CST

I run a md in order to understand the structure of the mdcrd and restart
files. I also created mdvel and mden files. I want to learn which rows
include velocity and periodic box informations. My sander input file is in
below. Could you please explain the the meaninig of other rows that I signed
in mdcrd, restart and mdvel files ?

Thanks in advance.

restart file

 3800 0.2000000E+02

     X(i) Y(i) Z(i) (?) (?) (?)
  36.3479317 14.4509277 26.0618370 36.1447649 13.5550616 27.3586499
  36.7353977 14.1962710 28.5981143 38.2583283 13.8880686 28.7062428
  38.4880248 12.5628497 29.4963986 39.9116357 12.0666737 29.6603785

mdcrd file

      X(i) Y(i) Z(i) (?) (?) (?) (?) (?)
(?) (?)
  39.211 17.741 25.929 40.440 18.641 25.822 41.313 18.245 27.012 42.436
  19.234 27.258 43.476 18.692 28.255 44.380 19.854 28.714 45.425 19.382
  29.739 46.155 20.559 30.418 47.283 20.019 31.303 47.945 21.161 32.093
  49.049 20.572 32.995 49.516 21.575 34.053 38.462 18.025 25.186 39.503
  16.705 25.745 38.747 17.778 26.916 40.145 19.690 25.885 40.965 18.464

mdvel

  X(i) Y(i) Z(i) (?) (?) (?) (?) (?) (?) (?)

 0.144 0.077 0.239 0.112 -0.008 -0.009 0.050 0.076 -0.020 0.009
 0.028 -0.038 -0.008 -0.035 -0.040 -0.187 0.015 0.197 -0.171 0.204
 0.258 -0.192 0.269 0.266 -0.027 0.050 0.039 -0.058 0.096 0.093
 0.158 0.187 -0.120 0.068 0.190 -0.137 -0.225 0.402 0.723 -0.074

MD equilibration
 &cntrl
  imin=0, irest=0, nstlim=10000, dt=0.002, ntx=1,
  ntc=2, ntf=2, ntpr=500, ntwx=500, ntwr=500,ntwe=500, ntwv=500,
  cut=9.825, ntb=2, ntp=1, ntr=0, ntt=1,taup=2.0, pres0=1,
  tempi=0.0, temp0=273.0,
 /

MD info

NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 270.72 PRESS =
-417.6
 Etot = 4193.2773 EKtot = 2366.3026 EPtot =
1826.9748
 BOND = 348.3747 ANGLE = 1656.8419 DIHED =
783.6537
 1-4 NB = 458.0015 1-4 EEL = 400.3209 VDWAALS =
-1392.3702
 EELEC = -427.8478 EHBOND = 0.0000 RESTRAINT =
0.0000
 EKCMT = 91.6470 VIRIAL = 474.7952 VOLUME =
42491.3448
                                                    Density =
0.6656
 Ewald error estimate: 0.2795E-04

2009/2/1 Carlos Simmerling <carlos.simmerling_at_gmail.com>

> have you looked at the section on file formats on the Amber web page? if
> yes, then tell us either what isn't clear or which formats you need that
> aren't there.
>
> On Sun, Feb 1, 2009 at 6:13 AM, oguz gurbulak <gurbulakoguz_at_gmail.com
> >wrote:
>
> > Dear All,
> > I'm planning to make analysis without using ptraj. So I want to learn the
> > structure of the output files (restrt, mdcrd, mdvel, mden ) and meaning
> of
> > the colums and rows in these output files. Because there are only numbers
> > in
> > these files. And I didn't find any explanations about the structure of
> the
> > output files. Can I easily learn the informations of the atom's xyz
> > coordinates, velocities and accelerations in any time step and ''pressure
> > tensors'' ? Or Should I write a script in order to get these informations
> ?
> > *Could** **you* please help me to get to know more about this issue ?
> And
> > I want to ask a question.
> >
> > For example
> >
> > > NSTEP = 2000 Density = 0.7636
> > >
> > > .
> > >
> > > .
> > >
> > > .
> > >
> > >
> > > NSTEP = 2500 Density = 0.7689
> >
> > I want to get the output informations for NSTEP = 2000 in target Density
> > =0.7636 for input and start a md from this point with little time steps.
> Is
> > it possible to do this in Amber? If so, what should I do to do this
> > operation *I**'**m looking forward to** **waiting** **for** *your*
> > **suggestions
> > ?**
> >
> > *
> >
> > Thanks in advance.
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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