[gmx-users] Analysis programs and PBC.

David van der Spoel spoel at xray.bmc.uu.se
Sun Feb 26 22:34:47 CET 2006

Maxim Fedorov wrote:
> 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 
> removal
> (even with modern scripting languages a human being should take a look 
> on the final results, isn't it :-)).

In all programs were it is needed PBC is taken care of. I have recently 
built in flags into some of the programs that allow you to control the 
removal of periodic boundary conditions (i.e. putting whole molecules in 
the box prior to analysis). The reason for this is that we're doing 
extensive simulations in vacuo, and putting the molecules back in the 
box breaks the analysis. In solvent the default behavior is fine.

Bottom line is that PBC is treated properly as far as I know. But you 
should always check your output :).

> With kindest regards,
> Maxim.
> Maxim V. Fedorov
> Research Associate.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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