[gmx-users] How to measure distance and find salt bridges in GROMACS ?

[Dallas Warren]

Good page to have a thorough read of is
http://manual.gromacs.org/documentation/current/user-guide/cmdline.html

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-distance.html

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-saltbr.html

Try some things, see what you can get out of them. It's the best way
to learn and see if getting what you want. Running the scripts and
looking at the results is much faster than posting to the emailing
list.

If doesn't give what you want, then reply with exactly what you are
wanting to generate, the exact command you executed (copy and paste
it), then the output you got (may need to host the images somewhere)
and why it isn't what you want/expect.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Fri, 14 Jun 2019 at 04:40, Vikram Dalal <vikram.dalal.37 at gmail.com> wrote:
>
> Hi all,
>
> I want to measure distance between two specific residues during molecular
> dynamics in GROMACS.
> I am not aware of gmx distance command for distance calculations.
>
> Second, I would like to know how to find the salt bridges during the period
> of molecular simulation.
>
>
>
> Thank you in advance.
> --
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