[gmx-users] Analysis programs and PBC.

David van der Spoel spoel at xray.bmc.uu.se
Mon Feb 27 09:08:49 CET 2006

Daniela S. Mueller wrote:
> Dear Maxim, dear David, 
> On Sun, 2006-02-26 at 22:34 +0100, David van der Spoel wrote:
>> 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 :).
> If the molecule you want to analyse is a single molecule, the jumping of
> box boundaries does not matter and the analysis tools take that into
> account. But if your molecule is a complex of two or more separate
> subunits, you might want to remove jumps over the boundaries to
> reassemble the complex again, e.g. to measure the minimum distance to
> the periodic images (and not to the subunit, which should be very
> nearby). 
> What I actually found with trjconv -pbc nojump was, that two conditions
> apply if you want to remove jumps: 1) the trajectory has to start at the
> initial frame and be continuous; 2) the tpr-file should correspond to
> the initial conformation. If these conditions weren't fulfilled, one of
> the subunits was rotated and the complex was reassembled incorrectly -
> although the box was rectangular. 
> This incorrect rotation seems to be a weird bug, probably the
> referencing to the tpr-structure is a special case-treatment and not
> robust to various setups...? 


if you have a reproducible case for this, please submit a bugzilla.

> Success and best regards, 
> Daniela
>>> With kindest regards,
>>> Maxim.
>>> Maxim V. Fedorov
>>> Research Associate.

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

More information about the gromacs.org_gmx-users mailing list