[gmx-users] Analysis programs and PBC.

Maxim Fedorov maxim.fedorov at ucd.ie
Sun Feb 26 22:10:00 CET 2006

Dear all,

I have been successfully using Gromacs for a couple years without 
bothering you -
manual + reading the mailing list was completely enough.

But … this is the second mail for this afternoon.

The question is: are there any analysis programs in GROMACS package 
which are sensitive to Periodic Boundary Conditions or they remove the 
periodicity automatically?

Now I explain in more details what I mean:

Let’s suppose that I have a trajectory file after some MD run with 
PBC. No shuffling, sorting and other things like that – only PBC.

Then I am going to analyze the trajectory with g_rama, g_hbond, g_rdf, 
g_gyrate and, very probably, something else.
Should I remove the periodicity first or I will be able to analyze the 
trajectory without bothering myself about that issue?
I have already tried to analyze the PBC runs with and without removal 
of periodicity– the results are the same. 
But may be this is only due to the fact that my molecule didn’t move 
too much during the run and was placed as a whole in the periodic 
cell? And, in a general case I have to remove the periodicity to be 
100% in the result of analysis.

Sorry, for this, probably, silly question, but I am starting several 
series of simulations - I will be not physically able to check every 
time several hundreds of trajectories with or without periodicity 
(even with modern scripting languages a human being should take a look 
on the final results, isn't it :-)).

With kindest regards,


Maxim V. Fedorov
Research Associate.

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