[gmx-users] Fwd: Re: Frequency dependent dielectric constant

[David van der Spoel]

On 2014-11-06 22:28, David van der Spoel wrote:
>
>
>
> -------- Original Message --------
> Subject:     Re: [gmx-users] Frequency dependent dielectric constant
> Date:     Thu, 6 Nov 2014 16:23:34 -0500
> From:     Bharat Sharma <bharatsolbridge at gmail.com>
> To:     spoel at xray.bmc.uu.se
>
>
>
> Hello Professor David,
> Sorry for sending you a private email.
> Thank you for your reply on forum. Is it possible to use external dipole
> moment file which has" t Mx My Mz " data to calculate autocorrelation
> function which is defined as phi (t) =  <M(t). M(o)>/ <M(0)>^2.
> Autocorrelation file is necessary to use g_dielectric function.
>
Looks like you have not run
gmx dielectric -h
You need the acf which you can produce using gmx dipoles

> Thank you.
>
> Sincerely,
> Bharat Sharma
>
> I have a file like this.
>
> 1  -18.4054002593869  -8.63550624406573  13.1822307410726
> 2  -16.3448281386543  -9.26825538523777  12.6970594193942
> 3  -16.2122319636283  -9.584079278168  10.1880749346946
> 4  -16.8000261232119  -9.3544161158981  9.292811661397
> 5  -16.9675609841484  -8.06386828149236  9.04336117783739
> 6  -16.705420659386  -8.15253302392368  6.35375835558321
> 7  -16.3482274903309  -7.42833201686778  2.40403368273462
> 8  -17.6089611732605  -6.58105246244449  1.01933331769956
> 9  -19.1340573022822  -7.31608247201016  1.0593505375146
> 10  -18.8898972984193  -8.50162965184524  -0.390241915321422
> 11  -17.3201971209895  -8.88827721892198  -2.91666461388975
> 12  -17.9697387584415  -10.3820791259894  -3.09327709524195
> 13  -19.4150366450719  -12.5922697307389  -1.76640044899152
> 14  -17.2192770802751  -12.719093017379  -1.76633521518987
> 15  -13.9887596873511  -11.6333686786579  -2.53760673124873
> 16  -15.631174760539  -11.8671822022606  -1.04251159658716
> 17  -19.7752453695527  -13.1793702340658  0.669842005269544
> 18  -20.5031312769212  -12.8221354246758  1.7010916111
> 19  -20.1714747689171  -11.5235359847683  3.12874014505405
> 20  -23.4993319248317  -11.1069526872016  5.40262656219366
> 21  -26.9810468267155  -10.3960073112131  6.66596873251908
> 22  -25.2970021256126  -8.26285916407095  6.85639239972755
> 23  -22.3727114023644  -7.29618209094124  7.96149529066325
> 24  -22.8378886264605  -7.94207228198017  9.4631219697683
> 25  -23.9479347882939  -8.18332794071831  8.90226933404197
> 26  -23.4431023794441  -8.57868882479158  7.48452761101869
> 27  -23.8923601075312  -9.80575680710948  7.74832733959732
> 28  -26.2650526524463  -11.6213772988559  7.80737869303804
> 29  -28.726262739164  -11.5765264683748  3.98968339600384
> 30  -28.8118374367959  -10.5568670286443  1.98998557532743
>
>
>
> On Thu, Nov 6, 2014 at 2:08 PM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
>      On 2014-11-06 19:33, Bharat Sharma wrote:
>
>          Hello,
>
>          It's a friendly reminder if someone knows how to calculate.
>          Please let me
>          know.
>
>      g_dielectric.
>
>
>          Thank you.
>
>          Bharat
>
>
>
>      --
>      David van der Spoel, Ph.D., Professor of Biology
>      Dept. of Cell & Molec. Biol., Uppsala University.
>      Box 596, 75124 Uppsala, Sweden. Phone: +46184714205
>      <tel:%2B46184714205>.
>      spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>      http://folding.bmc.uu.se
>      --
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se