[gmx-users] memory problems with g_hbond

[Attilio Vargiu]

Hi all,
I have some problems with memory in analyzing the h-bonds between a
molecule and waters. This is an extract of the output:
------------------------
Select a group: 65
Selected 65: 'O9_IMI'
Select a group: 9
Selected 9: 'WAT'
Checking for overlap...
Calculating hydrogen bonds between two groups of 1 and 24078 atoms
Found 0 donors and 1 acceptors in group 'O9_IMI'
Found 8026 donors and 8026 acceptors in group 'WAT'
Going to allocate 1509953 kb of memory, and that's only the beginning
Killed
-------------------------

Does someone know how to fix this problem? Is there some possibility
(for example with trjconv) to reduce the size of the box removing some
water molecule?

Thanks in advance, any help will be greatly apprecied!!!!

Attilio

---------
Attilio Vittorio Vargiu
Ph.D. Student at SISSA/ISAS, via Beirut 4 34014 Trieste, Italy
Phone: [phone], Fax : [phone]





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[David]

Post by Attilio Vargiu
Hi all,
I have some problems with memory in analyzing the h-bonds between a
------------------------
Select a group: 65
Selected 65: 'O9_IMI'
Select a group: 9
Selected 9: 'WAT'
Checking for overlap...
Calculating hydrogen bonds between two groups of 1 and 24078 atoms
Found 0 donors and 1 acceptors in group 'O9_IMI'
Found 8026 donors and 8026 acceptors in group 'WAT'
Going to allocate 1509953 kb of memory, and that's only the beginning
Killed
-------------------------
Does someone know how to fix this problem? Is there some possibility
(for example with trjconv) to reduce the size of the box removing some
water molecule?

You must make an index group where you divide the waters in groups, e.g.
2 groups of half the molecules, then do the analysis on the groups and
combine the results.

Post by Attilio Vargiu
Thanks in advance, any help will be greatly apprecied!!!!
Attilio
---------
Attilio Vittorio Vargiu
Ph.D. Student at SISSA/ISAS, via Beirut 4 34014 Trieste, Italy
Phone: [phone], Fax : [phone]
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[Attilio Vargiu]

Many thanks for the suggestion!!!

Attilio

Post by David

Post by Attilio Vargiu
Hi all,
I have some problems with memory in analyzing the h-bonds between a
------------------------
Select a group: 65
Selected 65: 'O9_IMI'
Select a group: 9
Selected 9: 'WAT'
Checking for overlap...
Calculating hydrogen bonds between two groups of 1 and 24078 atoms
Found 0 donors and 1 acceptors in group 'O9_IMI'
Found 8026 donors and 8026 acceptors in group 'WAT'
Going to allocate 1509953 kb of memory, and that's only the beginning
Killed
-------------------------
Does someone know how to fix this problem? Is there some possibility
(for example with trjconv) to reduce the size of the box removing some
water molecule?

You must make an index group where you divide the waters in groups, e.g.
2 groups of half the molecules, then do the analysis on the groups and
combine the results.

Post by Attilio Vargiu
Thanks in advance, any help will be greatly apprecied!!!!
Attilio
---------
Attilio Vittorio Vargiu
Ph.D. Student at SISSA/ISAS, via Beirut 4 34014 Trieste, Italy
Phone: [phone], Fax : [phone]
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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: [phone] fax: [phone]
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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[Anton Feenstra]

Post by Attilio Vargiu
Many thanks for the suggestion!!!

You could also use trjorder to sort the water molecules on their
distance to the solute. Then, you can take the first half (or so) water
molecules, which will be in a 'shell' around the solute. That should be
enough for analysis of h-bonding. (but, you may loose the time
correlation of h-bonding, since the sorting will differ for each frame).
--
Groetjes,

Anton

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