Yah but you'll have to smooth it, mean wise, or beter averidge several runs. qtiplot or equivalent will work (even MS Excell if you have the added mean determination formulas).
Stephan Watkins
Gesendet: Mittwoch, 21. Mai 2014 um 06:54 Uhr
Von: "tarak karmakar" <[email protected]>
An: "Discussion list for GROMACS users" <[email protected]>
Betreff: Re: [gmx-users] entropy vs time plot
Von: "tarak karmakar" <[email protected]>
An: "Discussion list for GROMACS users" <[email protected]>
Betreff: Re: [gmx-users] entropy vs time plot
Hi Tsjerk,
Thanks for the quick reply.
I did the following
g_covar -f ../../npt_prod -s ../../npt_prod -n loop_II.ndx -o eigenval -v
eigenvec.trr -av average.pdb -b 0 -e 10000
g_anaeig -v eigenvec -entropy -temp 300 -b 0 -e 10000
What I want to plot is similar to this.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304994/figure/fig4/
Is there any flag for this?
I've checked g_covar -h and g_anaeig -h but didn't get the proper way.
Thanks,
Tarak
On Tue, May 20, 2014 at 11:04 PM, Tsjerk Wassenaar <[email protected]>wrote:
> Hi Tarak,
>
> You will have to use -b/-e to set the start and end times.
>
> Cheers,
>
> Tsjerk
>
>
> On Tue, May 20, 2014 at 12:18 PM, tarak karmakar <[email protected]
> >wrote:
>
> > Dear All,
> > Could anyone tell me how to plot configurational entropy as a function of
> > simulation time?
> > Do I need to manually specify the -dt(say after each 1 ns) during the
> > g_covar and then do g_anaeig in each of the step?
> >
> > thanks,
> > Tarak
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> > send a mail to [email protected].
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
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Thanks for the quick reply.
I did the following
g_covar -f ../../npt_prod -s ../../npt_prod -n loop_II.ndx -o eigenval -v
eigenvec.trr -av average.pdb -b 0 -e 10000
g_anaeig -v eigenvec -entropy -temp 300 -b 0 -e 10000
What I want to plot is similar to this.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304994/figure/fig4/
Is there any flag for this?
I've checked g_covar -h and g_anaeig -h but didn't get the proper way.
Thanks,
Tarak
On Tue, May 20, 2014 at 11:04 PM, Tsjerk Wassenaar <[email protected]>wrote:
> Hi Tarak,
>
> You will have to use -b/-e to set the start and end times.
>
> Cheers,
>
> Tsjerk
>
>
> On Tue, May 20, 2014 at 12:18 PM, tarak karmakar <[email protected]
> >wrote:
>
> > Dear All,
> > Could anyone tell me how to plot configurational entropy as a function of
> > simulation time?
> > Do I need to manually specify the -dt(say after each 1 ns) during the
> > g_covar and then do g_anaeig in each of the step?
> >
> > thanks,
> > Tarak
> > --
> > 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].
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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> send a mail to [email protected].
>
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-- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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