On 2014-05-21 06:54, tarak karmakar wrote:
Hi Tsjerk, Thanks for the quick reply. I did the followingg_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.
You need to run a
for($N=1000; ($N<=10000); $N+= 100) {
g_covar -e $N
g_anaeig
grep S from standard out and save it
}
Thanks, Tarak On Tue, May 20, 2014 at 11:04 PM, Tsjerk Wassenaar <tsje...@gmail.com>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 <tarak20...@gmail.comwrote: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 gmx-users-requ...@gromacs.org.-- 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! * 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 gmx-users-requ...@gromacs.org.
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