Re: [gmx-users] density graph ( density vs time)
Jochen Hub wrote: huan wrote: I used g_energy before but i just obtained density (y-axis) versus box length (x axis). huan wrote: Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. Sounds like a contradition to me... :-) Indeed; the g_energy output gives the x-axis as time... -Justin thanks --- On Tue, 10/28/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: From: Justin A. Lemkul <[EMAIL PROTECTED]> Subject: Re: [gmx-users] density graph ( density vs time) To: [EMAIL PROTECTED], "Discussion list for GROMACS users" Date: Tuesday, October 28, 2008, 11:31 PM huan wrote: Dear all, Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. So now i wonder is it there is another way that we can use other way to obtain a density (y axis) versus time length (x-axis). Use g_energy. -Justin Thanks.. --- On Tue, 10/28/08, Mark Abraham <[EMAIL PROTECTED]> wrote: From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] density graph ( density vs time) To: "Discussion list for GROMACS users" Date: Tuesday, October 28, 2008, 4:46 PM huan wrote: Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Please ask a more specific question. We can't tell whether your problem is knowing what tool to use, how to use it, how to label axes of plots or something else. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] density graph ( density vs time)
huan wrote: > I used g_energy before but i just obtained density (y-axis) versus box length (x axis). huan wrote: > Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. Sounds like a contradition to me... :-) > > thanks > > --- On Tue, 10/28/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > >> From: Justin A. Lemkul <[EMAIL PROTECTED]> >> Subject: Re: [gmx-users] density graph ( density vs time) >> To: [EMAIL PROTECTED], "Discussion list for GROMACS users" >> >> Date: Tuesday, October 28, 2008, 11:31 PM >> huan wrote: >>> Dear all, >>> >>> Previously i obtained a density (y-axis) versus box >> length (x axis) using g_density.. >>> So now i wonder is it there is another way that we can >> use other way to obtain a density (y axis) versus time >> length (x-axis). >> Use g_energy. >> >> -Justin >> >>> Thanks.. >>> >>> >>> --- On Tue, 10/28/08, Mark Abraham >> <[EMAIL PROTECTED]> wrote: >>>> From: Mark Abraham <[EMAIL PROTECTED]> >>>> Subject: Re: [gmx-users] density graph ( density >> vs time) >>>> To: "Discussion list for GROMACS users" >> >>>> Date: Tuesday, October 28, 2008, 4:46 PM >>>> huan wrote: >>>>> Dear all gmx-users and developers. >>>>> >>>>> I wish to get a density graph with density >> versus time >>>> instead of nm, so how can i obtained this? >>>> >>>> Please ask a more specific question. We can't >> tell >>>> whether your problem >>>> is knowing what tool to use, how to use it, how to >> label >>>> axes of plots >>>> or something else. >>>> >>>> Mark >>>> ___ >>>> gmx-users mailing listgmx-users@gromacs.org >>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >> http://www.gromacs.org/search >>>> before posting! >>>> Please don't post (un)subscribe requests to >> the list. >>>> Use the >>>> www interface or send it to >> [EMAIL PROTECTED] >>>> Can't post? Read >>>> http://www.gromacs.org/mailing_lists/users.php >>> >>> >>> ___ >>> gmx-users mailing listgmx-users@gromacs.org >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >> http://www.gromacs.org/search before posting! >>> Please don't post (un)subscribe requests to the >> list. Use the >>> www interface or send it to >> [EMAIL PROTECTED] >>> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> -- >> >> >> Justin A. Lemkul >> Graduate Research Assistant >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > . > -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] density graph ( density vs time)
I used g_energy before but i just obtained density (y-axis) versus box length (x axis). now i wish to obtain density vs time thanks --- On Tue, 10/28/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] density graph ( density vs time) > To: [EMAIL PROTECTED], "Discussion list for GROMACS users" > > Date: Tuesday, October 28, 2008, 11:31 PM > huan wrote: > > Dear all, > > > > Previously i obtained a density (y-axis) versus box > length (x axis) using g_density.. > > > > So now i wonder is it there is another way that we can > use other way to obtain a density (y axis) versus time > length (x-axis). > > > > Use g_energy. > > -Justin > > > Thanks.. > > > > > > --- On Tue, 10/28/08, Mark Abraham > <[EMAIL PROTECTED]> wrote: > > > >> From: Mark Abraham <[EMAIL PROTECTED]> > >> Subject: Re: [gmx-users] density graph ( density > vs time) > >> To: "Discussion list for GROMACS users" > > >> Date: Tuesday, October 28, 2008, 4:46 PM > >> huan wrote: > >>> Dear all gmx-users and developers. > >>> > >>> I wish to get a density graph with density > versus time > >> instead of nm, so how can i obtained this? > >> > >> Please ask a more specific question. We can't > tell > >> whether your problem > >> is knowing what tool to use, how to use it, how to > label > >> axes of plots > >> or something else. > >> > >> Mark > >> ___ > >> gmx-users mailing listgmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > http://www.gromacs.org/search > >> before posting! > >> Please don't post (un)subscribe requests to > the list. > >> Use the > >> www interface or send it to > [EMAIL PROTECTED] > >> Can't post? Read > >> http://www.gromacs.org/mailing_lists/users.php > > > > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the > list. Use the > > www interface or send it to > [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > -- > > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] density graph ( density vs time)
huan wrote: Dear all, Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. So now i wonder is it there is another way that we can use other way to obtain a density (y axis) versus time length (x-axis). Use g_energy. -Justin Thanks.. --- On Tue, 10/28/08, Mark Abraham <[EMAIL PROTECTED]> wrote: From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] density graph ( density vs time) To: "Discussion list for GROMACS users" Date: Tuesday, October 28, 2008, 4:46 PM huan wrote: Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Please ask a more specific question. We can't tell whether your problem is knowing what tool to use, how to use it, how to label axes of plots or something else. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] density graph ( density vs time)
Dear all, Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. So now i wonder is it there is another way that we can use other way to obtain a density (y axis) versus time length (x-axis). Thanks.. --- On Tue, 10/28/08, Mark Abraham <[EMAIL PROTECTED]> wrote: > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] density graph ( density vs time) > To: "Discussion list for GROMACS users" > Date: Tuesday, October 28, 2008, 4:46 PM > huan wrote: > > Dear all gmx-users and developers. > > > > I wish to get a density graph with density versus time > instead of nm, so how can i obtained this? > > Please ask a more specific question. We can't tell > whether your problem > is knowing what tool to use, how to use it, how to label > axes of plots > or something else. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > Please don't post (un)subscribe requests to the list. > Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] density graph ( density vs time)
huan wrote: > Dear all gmx-users and developers. > > I wish to get a density graph with density versus time instead of nm, so how > can i obtained this? You could extract the box vectors with g_energy and compute the density from the volume. Best, Jochen > > Thanks. > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > . > -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] density graph ( density vs time)
huan wrote: Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Please ask a more specific question. We can't tell whether your problem is knowing what tool to use, how to use it, how to label axes of plots or something else. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] density graph ( density vs time)
Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
