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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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