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 <[email protected]> To: [email protected] 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 <[email protected] <mailto:[email protected]>> 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>. [email protected] <mailto:[email protected]> http://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/GMX-__Users_List <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before posting! * Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists <http://www.gromacs.org/Support/Mailing_Lists> * For (un)subscribe requests visit https://maillist.sys.kth.se/__mailman/listinfo/gromacs.org___gmx-users <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> or send a mail to [email protected] <mailto:[email protected]>.
-- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. [email protected] http://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
