[gmx-users] How to choose z component of two groups

[Christopher Neale]

I believe it is like this

time x1 y1 z1 x2 y2 z2 ... xN yN zN

so you want to average like this:

cat thickness.xvg | grep -v '[#|@]' | awk '{s=0;for(i=4;i<=NF;i+=3){s+=$i;n++};avg=s/n;print $1,avg}'

Obviously do a sanity check on the output. Still, I agree that the comments at the top of thickness.xvg could be more useful. I'll file a redmine request to improve that

Chris.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Мижээ Батсайхан <b.mijiddorj at gmail.com>
Sent: 07 February 2017 22:47:24
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] How to choose z component of two groups

Dear Justin,
Thank you very much for your reply.

I have a confusion. There are 66 columns in thickness.xvg, and no header of
the columns.
How can I know the columns of z component? I think there are number of
columns corresponding to x and y components.
I averaged the all column, the values are too small and minus.

Mijiddorj

>
> On 2/6/17 9:13 PM, ????? ????????? wrote:
> > Dear Justin,
> >
> > Thank you very much for your reply.
> >
> > I inspected the thickness.xvg. There are number of columns in this file,
> I
> > could not realize that which one is Z component of thickness.
> > I also got averaged values using -oav option. How can I get the averaged
> > values of Z component?
> >
>
> Average the column of thickness.xvg that corresponds to the Z-dimension.
>
> -Justin
>
> >
> > Best regards,
> >
> > Mijiddorj
> >
> >
> >
> > Dear gmx users,
> >
> > I am performing analysis of membrane system. I would like to estimate
> > membrane thickness.
> >
> > I toke following command:
> >
> > gmx distance 0s topol.tpr -f traj.xtc -n selected_P.ndx -oav ave.xvg
> -oxyz
> > thickness.xvg
> >
> >
> > I do not know how to select z component of the two groups.
> >
> > Is there any advice, please?
> >
> >
> > Have you inspected the contents of thickness.xvg? I suspect you'll find
> > exactlywhat you're looking for.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> > jalem... at outerbanks.umaryland.edu | (410)
> > 706-7441http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
--
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-request at gromacs.org.