How to find contacts/dist between a specified atom/residue and unspecified lipid residues?

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1

GROMACS version:2019
GROMACS modification: Yes/No
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Friends,

I have a multi species system trajectory (memb protein).

I want to know,

Hi,

I have set up a protein and a membrane.
Residues of protein is R1, R2, R3
Lipids are DPC, DPE 10,000 atoms
I have already created index files with above protein residues
But given the large number of lipid residues, it’s not possible to define one at a time.
In my thinking, gmx sure has some solution for this.

Which gmx function can be used to find out which DPC, DPE lipid atoms/residues (by residue id, name, atom name) interact most with protein residue R1, R2, R3?

I tried mindist, contacts. But it only showed minimum distance between residue and lipid groups.
It doesn’t show the contacts by lipid residue name and id. (at least from what I have done so far).

I would also like to know how long a particular protein residue (atom) and lipid contact lasts.

Thanks in advance for your suggestions.

2

Hi, I have exactly the same question: I also want to count contact between specified atoms in the system. Did you find a solution afterwards? Thanks.

3

Hi,

did you try gmx mindist with the option -d {value} and -o?
The log file will provide information on the atoms in contact.

If you are interested in the time series of a distance between 2 defined atoms/molecules, you can use the information in log file to generate a new index file and then calculate the desired time series using gmx distance, gmx mindist and gmx pairdist (depending on the cases)

I hope it helps
Alessandra