Marta Murcia wrote:
Dear all,
I am running a series of AFM simulations starting from different
conformations taken from a trajectory (gmx 3.3). Everything works fine,
but if I try to orient all the snapshots with respect to a reference
(based on the protein superimposition) I get segmentation fault for all
of them while doing mdrun, except for the one that I used as template in
the alignment. My feeling is that the box of water molecules is not
being well understand. I was using the same topology files as before but
this shouldn't affect (should be?). Do I need to do pdb2gmx again for
the individual gro files. Does it have something to do with genbox? What
is wrong?
Guys I really appreciate your help, I don't know what to do but I'd bet
there is something really stupid I am missing
it's not clear what you are doing. how can you "orient snapshots in mdrun"?
Thanks so much
M
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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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