AMBER Archive (2009)

Subject: Re: [AMBER] the output files

From: oguz gurbulak (gurbulakoguz_at_gmail.com)
Date: Tue Feb 10 2009 - 08:11:44 CST

Dear Carlos,

Thank you very much for your explanation. But I think velocity and periodic
box information can be written to 'restrt', mdcrd, mdvel versions according
to the sander input file options. If so, what is the order of velocity and
periodic box information after x1, y1, z1, x2, y2, z2, ...
coordinates informations
?

Thank you very much for your attention.

Kind regards.

2009/2/10 Carlos Simmerling <carlos.simmerling_at_gmail.com>

> the files are always x1, y1, z1, x2, y2, z2, etc. they go in order
> regardless of 6 or 10 numbers per column.
> with 6 columns, it has xyz for 2 atoms in each row. with 10, it has
> x1y1z2x2y2z2x3y3z3x4
> and then the next row starts with x5.
> if you write programs this should be clear, it is just read or written with
> a format statement that specifies # of values in each row and their format.
> if you don't know how to write programs, doing uncommon analysis can be
> difficult. I don't know of any code that calculates stress tensors. ptraj
> is
> pretty well documented, so if it isn't in the manual then likely the
> feature
> is not included.
>
>
> On Tue, Feb 10, 2009 at 6:14 AM, oguz gurbulak <gurbulakoguz_at_gmail.com
> >wrote:
>
> > 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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