AMBER Archive (2009)

Subject: Re: [AMBER] the output files

From: oguz gurbulak (gurbulakoguz_at_gmail.com)
Date: Tue Feb 10 2009 - 05:14:58 CST

Dear Carlos,

I examined the Amber file formats as you said and I still have some
questions that I want to learn in details. Firstly, according to the file
formats for 'restrt' version created as a result of energy minimization or
molecular dynamics includes six colums. Could you explain the types of
information ( coordinates, velocity and periodic box information ) of these
colums ? Secondly for mdcrd, mdvel version created by molecular dynamics
includes ten colums. I think Amber file formats have an information writing
order. So, generally What are the types of information ( coordinates,
velocity and periodic box information ) of these ten colums ? And I also
asked a question to mail archive about analysis but I didn't get an answer
to this question. Can I calcuate Mean square displacements ( MSD ) and
autocorrelation functions of the stress tensors using ptraj or other
analysis tools in Amber 10 ? I'm eagerly waiting for your suggestions.

Thank you very much for your attention.

Kind regards.

2009/2/9 Carlos Simmerling <carlos.simmerling_at_gmail.com>

> have you looked at the file formats page on the amber web site? it has
> this information.
> please be specific about which parts of that page are unclear.
> your assignments are not correct- but the format page is easier to
> understand if you have done some programming. let us know if you have
> or not, and how you plan to process files. right now it's hard to help
> you since we don't have enough information about what you want to do
> and what skills you have so we know what would be a practical
> suggestion.
>
>
> On Mon, Feb 9, 2009 at 8:03 AM, oguz gurbulak <gurbulakoguz_at_gmail.com>
> wrote:
> > 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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