# Contact map for membrane

**URL:** <https://gromacs.bioexcel.eu/t/contact-map-for-membrane/11548>\
**Category:** User discussions\
**Created:** [February 14, 2025, 3:34pm UTC](https://gromacs.bioexcel.eu/t/contact-map-for-membrane/11548 "2025-02-14T15:34:49Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![SAHIRE](https://avatars.discourse-cdn.com/v4/letter/s/b2d939/32.png) [@SAHIRE](https://gromacs.bioexcel.eu/u/SAHIRE)\
**Post date:** [February 14, 2025, 3:34pm UTC](https://gromacs.bioexcel.eu/t/contact-map-for-membrane/11548/1 "2025-02-14T15:34:49Z")

</div>

GROMACS version:  
GROMACS modification: Yes/No  
Here post your question  
I have a lipid bilayer composed of three different components. Could you guide me on how to generate a contact map for these lipids using GROMACS?

---

<div class="post-metadata">

**Author:** ![H.Mosaddeghi](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/h.mosaddeghi/32/4066_2.png) [@H.Mosaddeghi](https://gromacs.bioexcel.eu/u/H.Mosaddeghi)\
**Post date:** [February 14, 2025, 8:10pm UTC](https://gromacs.bioexcel.eu/t/contact-map-for-membrane/11548/2 "2025-02-14T20:10:05Z")

</div>

you can use thes methods:

Use gmx mdmat -f \*.xtc -s \*.tpr -mean mat.xpm -frames mat1.xpm -no mat.xvg -n index.ndx (Index specific group for contact analysis)  
xpm2ps -f \*.xpm -o \*.eps -rainbow blue

or

use vmd \>\>\> [Contact Map Plugin, Version 1.0](https://www.ks.uiuc.edu/Research/vmd/plugins/contactmap/)

or

use Mdanalysis \>\> [4.3.2. Native contacts analysis — MDAnalysis.analysis.contacts — MDAnalysis 2.8.0 documentation](https://docs.mdanalysis.org/stable/documentation_pages/analysis/contacts.html)

---

<div class="post-metadata">

**Author:** ![SAHIRE](https://avatars.discourse-cdn.com/v4/letter/s/b2d939/32.png) [@SAHIRE](https://gromacs.bioexcel.eu/u/SAHIRE)\
**Post date:** [February 16, 2025, 10:22pm UTC](https://gromacs.bioexcel.eu/t/contact-map-for-membrane/11548/3 "2025-02-16T22:22:03Z")

</div>

Could you tell me how to find the contact map for each lipid in a multi-component lipid bilayer using VMD software?

---

<div class="post-metadata">

**Author:** ![SAHIRE](https://avatars.discourse-cdn.com/v4/letter/s/b2d939/32.png) [@SAHIRE](https://gromacs.bioexcel.eu/u/SAHIRE)\
**Post date:** [February 17, 2025, 10:51am UTC](https://gromacs.bioexcel.eu/t/contact-map-for-membrane/11548/4 "2025-02-17T10:51:06Z")

</div>

Hi Mosaddeghi,  
Is it possible to find Contact Map using Contact Map Plugin in VMD for multi component lipid system or it is only possible in the case of protein residues ?  
If it is possible then can you tell me how can I do it?