AMBER Archive (2009)

Subject: Re: [AMBER] the output files

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Feb 09 2009 - 07:06:41 CST

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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