[gmx-users] hbond calculation in peptide-membrane simulation

[Dallas Warren]

What have you tried?  What results did you get?

Highly recommend you try things out, experiment, see what happens.
That is faster and you learn more than having to wait for someone on
an emailing list to reply.  Search engine is very helpful too.

http://manual.gromacs.org/documentation/2016.4/onlinehelp/gmx-hbond.html
- "You need to specify two groups for analysis, which must be either
identical or non-overlapping. All hydrogen bonds between the two
groups are analyzed."

To make index groups -
http://manual.gromacs.org/documentation/2016.4/onlinehelp/gmx-make_ndx.html

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 Mon, 15 Oct 2018 at 18:15, manindersingh rajawat
<rajawat.manindersingh at gmail.com> wrote:
>
> Dear gromacs users,
> I performed 200ns MD simulations (gromacs 5.0.7) of peptide and mixed lipid
> bilayer (POPS:POPC). Initially placed 6 copies of the peptide parallely
> over the surface of the lipid bilayer (128 lipids). I want to calculate
> hydrogen bond occupancy using hbond tool between peptide and lipids over
> the simulation time. How to make index file for it. What atoms I should put
> in index file.
> Please advise with appropriate commands.
> Thanks and regards,
> Maninder
>
>
> --
> Maninder Singh
> Research Fellow,
> LSN-104, Computational Biology and Bioinformatics Unit,
> Molecular and Structural Biology Division,
> CSIR-Central Drug Research Institute,
> Sector-10, Janakipuram Extension,
> Sitapur road,
> Lucknow
> India-226031
> M: +919129206276
> Email: rajawat.manindersingh at gmail.com
> --
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