Hello,
I am trying to use the -surf option in gmx rdf in order to compute the rdf of certain molecules from the surface (nearest atoms) of my reference molecule .
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:
Hi, when you specify -ref and -sel you shall write the group numbers from the index file. In your case you wrote the text instead of them.
Inna Ermilova Thanks for your reply.
I don't need an index file, because I don't have unique groups that I'd like to measure. I'd like to measure my rdf from all URA and OCS residues.
Why is it wrong to write my text instead of them?
Hi, Ilan! Because the syntax of the command says that you shall put numbers of groups, not texts. That is why you get this error.
Inna Ermilova Writing a group through index file and then calling 'group 1' is the same as writing 'resname 1'. These are just different ways of telling gromacs which molecules to count. The way I call works fine as long as I dont use the -surf flag. I dont get an error with 'resname', I get the error with -surf.
Hi Ilan, let's say that you have groups 21 and 23 which are groups for your reference and selection respectively. So in the command line you shall write for those flags the following:
-ref 21 -sel 23
You shall process the command correctly if you don't want errors. By the way, the syntax which you used, the one which gave you errors,worked for VMD, but not for Gromacs.
Inna Ermilova
But I don't want to study only two molecules, but two types of molecules. So I need all the groups which have molecule type 1 in ref, and all groups of the other molecule type 2 in sel.
And the syntax I use works all the time when my rdf is radial. Only when using -surf flag it starts giving me errors.
By the way, this script works when I write:
gmx rdf -s tpr.tpr -ref ‘resname URA’ -sel ‘resname OCS’ -f xtc.xtc -surf mol -bin 0.03
where I just removed the " -seltype whole_mol_com". So this proves that my syntax is fine. However I get the following very weird looking radial distribution.
Now I need to figure out why it's not normalized. Any ideas?
By the way , thanks for all your support :)
Ilan, I didn't say that you will study only two molecules like that. Basically, you calculate exactly what you want to calculate. Since you can not obtain the result your script doesn't work. Also the normalized rdf shall the final value of 1 not about 4500. ;-) What do you mean by "when my rdf is radial"? The definition of rdf is "radial distribution function".
It is good that you removed the information about the center of mass because for "-surf" the routine does not support COM.
I still suggest you to write a proper index-file for your RDF-calculation which you will pass then after "-n" flag, because trp-file has the original information about your topology. In that index file you can separately put molecules which belong to a cluster/membrane (the ones which build surface), then all other molecules you put in another group. It can happen that you managed to pass the command, but then you can not be so sure about what you calculated. You shall try to verify that by inspecting your file RDF.xvg, then one which you are plotting. In the legend you shall see which groups the routine used for RDF-calculation.
Regarding, the normalization you shall add the flag and it will be normalized.
See more information about rdf-calculation: http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-rdf.html
I will try to change my syntax to the index you suggest. See if yields a different result.
However the 4500 i'm getting is an issue, and the -norm flag isn't working with the -surf flag:
gromacs error: "-surf cannot be combined with -norm"
So I am stuck with the default -norm which is called "rdf" normalization. Which gives me a 4500 rdf instead of 1. So it could be that gromacs doesnt know how to normalize with the -surf flag?
Or its the issue with my syntax? I'll check.
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