does the GRO file have all the connectivity information required to initiate MDAnalysis?

[Satyen Dhamankar]

Hello, 

I am running a simple simulation for benzene in GROMACS with 739 benzene molecules using the GROMOS forcefield. What I want to do is run some analysis on my trajectory. 

This is how I have set things up: 

import MDAnalysis

import numpy as np

u = MDAnalysis.Universe("739-c6h6-in-box.gro","739-c6h6-MolDynamics_good-pbc.xtc")

The above piece of code ran with no errors. 

.xtc is the binary gromacs trajectory file. 

.gro file contains all the coordinates of the 739 molecules, with the residue number, resid. 

As far as I know, my 739-c6h6-in-box.gro file, does not have information about connectivity. I created that file using the insert-molecules command in GROMACS using the file c6h6-in-box.gro. c6h6-in-box.gro was created using editconf on c6h6.pdb. 

My question is, since 739-c6h6-in-box.gro has no explicit mention of connectivity, will my analysis work fine? If not, how do I go about entering the topology of my file?

Thank you in advance for any advice you have for me!

[Sudarshan Behera]

Dear Satyen,

As long as your analysis involves atom selection using resid, atom name, residue name, and/or atom index, it will work fine as the GRO file contains this information. But, if you are doing an analysis that required you to select a group of atoms using segid (chain id) and others, it will not work. A better way is to load a PDB file instead of a GRO file. The best way is to load a TPR generated by gromacs (if you've). The TPR file has all the information.

Hope this helps.

Thank you. Regards

Sudarshan

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Sudarshan Behera

Ph.D. Graduate Student

Supervisor - Prof. S. Balasubramanian

Molecular Simulation Laboratory

JNCASR, Bangalore

INDIA

[Satyen Dhamankar]

Thank you for your response! I will try this out.