# Surface rdf **URL:** \ **Category:** User discussions\ **Created:** [September 23, 2020, 2:09pm UTC](https://gromacs.bioexcel.eu/t/surface-rdf/860 "2020-09-23T14:09:52Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![kosmith](https://avatars.discourse-cdn.com/v4/letter/k/f04885/32.png) [@kosmith](https://gromacs.bioexcel.eu/u/kosmith)\ **Post date:** [September 23, 2020, 2:09pm UTC](https://gromacs.bioexcel.eu/t/surface-rdf/860/1 "2020-09-23T14:09:52Z")
GROMACS version: 2018 GROMACS modification: Yes/No Hello, I am trying to use the -surf option in gmx rdf in order to compute the rdf of certain molecules from the surface of my reference molecule (nearest atoms). My script is: gmx rdf -s tpr.tpr -ref ‘resname URA’ -sel ‘resname OCS’ -f xtc.xtc -surf mol -seltype whole\_mol\_com -bin 0.03 Unfortunately, I get the following error: “Inconsistency in user input: -surf only works with -ref that consists of atoms” Obviously my molecule consists of atoms. And different scripts that don’t have the -surf flag work perfectly fine. Anyone has an idea what is the problem? Here are things I’ve tried but didn’t change the error: 1. I tried adding -selrpos whole\_mol\_com, same error. 2. I tried changing the molecules that I put under “resname X” but for any X it’s the same error. 3. I tried changing the order in which all my flags appear. 4. I tried doing -surf mol and -surf res. 5. I tried running this script on different gromacs versions. ---
**Author:** ![MarceloAlbuquerque](https://avatars.discourse-cdn.com/v4/letter/m/b782af/32.png) [@MarceloAlbuquerque](https://gromacs.bioexcel.eu/u/MarceloAlbuquerque)\ **Post date:** [September 23, 2020, 5:56pm UTC](https://gromacs.bioexcel.eu/t/surface-rdf/860/2 "2020-09-23T17:56:16Z")
Dear Kosmith, That means that you must use atoms as -seltype option. Please, check the following manual (gmx rdf), specifically the second to last paragraph. > **[gmx rdf — GROMACS 2018.3 documentation](http://manual.gromacs.org/documentation/2018.3/onlinehelp/gmx-rdf.html)** I hope it helps you. Best wishes, Marcelo Albuquerque PhD Student Physics Institute (IF-UFF) Universidade Federal Fluminense (UFF) Brazil - Niterói/RJ ---
**Author:** ![kosmith](https://avatars.discourse-cdn.com/v4/letter/k/f04885/32.png) [@kosmith](https://gromacs.bioexcel.eu/u/kosmith)\ **Post date:** [September 24, 2020, 5:23am UTC](https://gromacs.bioexcel.eu/t/surface-rdf/860/3 "2020-09-24T05:23:01Z")
Dear Marcelo, Thank you for your reply. Once I removed the -seltype flag, it works. Thanks for your help. I don’t know how you knew that was the issue. I read the documentation several times before. But the COM restrictions for -surf flag are only written for the -ref flag, not the -sel flag. Best, Ilan ---
**Author:** ![kosmith](https://avatars.discourse-cdn.com/v4/letter/k/f04885/32.png) [@kosmith](https://gromacs.bioexcel.eu/u/kosmith)\ **Post date:** [October 4, 2020, 6:58am UTC](https://gromacs.bioexcel.eu/t/surface-rdf/860/4 "2020-10-04T06:58:53Z")
Hello Marcelo, The code works now, but it causes some unnormalized-looking g® (see attached png file): ![g(r)](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/70ea16f707afde541a3b58563a8e5c9088c58565.png) gmx\_mpi rdf -s tpr.tpr -ref ‘resname TST’ -sel 'resname RER -f movie.xtc -o test.xvg -bin 0.03 -surf res Any idea why? And how do I fix this? Thanks again, Ilan ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [October 5, 2020, 12:51am UTC](https://gromacs.bioexcel.eu/t/surface-rdf/860/5 "2020-10-05T00:51:46Z")
How are TST and RER distributed with respect to each other within your simulation? [http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html](http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html) > For `-surf` , the selection provided to `-ref` must select atoms, i.e., centers of mass are not supported. Further, `-nonorm` is implied, as the bins have irregular shapes and the volume of a bin is not easily computable. > `none` : Use only the first factor. In this case, the RDF is only scaled with the bin width to make the integral of the curve represent the number of pairs within a range. In other words the RDF is not normalised. ---
**Author:** ![MarceloAlbuquerque](https://avatars.discourse-cdn.com/v4/letter/m/b782af/32.png) [@MarceloAlbuquerque](https://gromacs.bioexcel.eu/u/MarceloAlbuquerque)\ **Post date:** [October 5, 2020, 6:54pm UTC](https://gromacs.bioexcel.eu/t/surface-rdf/860/6 "2020-10-05T18:54:26Z")
I knew that because I had already done that once ago, when I was trying different options to see what would be the outcome. In fact, as far as I remember, the error you informed was the same I had gotten previously. That’s why I knew what to do. :) ---
**Author:** ![MarceloAlbuquerque](https://avatars.discourse-cdn.com/v4/letter/m/b782af/32.png) [@MarceloAlbuquerque](https://gromacs.bioexcel.eu/u/MarceloAlbuquerque)\ **Post date:** [October 5, 2020, 6:56pm UTC](https://gromacs.bioexcel.eu/t/surface-rdf/860/7 "2020-10-05T18:56:47Z")
I think you must specify an option of normalization, as @Dr_DBW has replied. ---
**Author:** ![kosmith](https://avatars.discourse-cdn.com/v4/letter/k/f04885/32.png) [@kosmith](https://gromacs.bioexcel.eu/u/kosmith)\ **Post date:** [October 6, 2020, 6:02am UTC](https://gromacs.bioexcel.eu/t/surface-rdf/860/8 "2020-10-06T06:02:51Z")
@Dr_DBW @MarceloAlbuquerque So what is the point of RDF with the -surf flag if it’s not normalized? What information does it give me? The -norm flag doesn’t work with -surf. My TST is just one molecule and RER is the solvent, so plenty of RER.