[gmx-users] NMA error

[David van der Spoel]

Fabrizio Mancinelli wrote:
> Hello all,
> excuse me if I re-post the same question, but I didn't got any answer so maybe 
> the post has been overlooked.
> In performing a NMA in vacuum of a large (~600 residue) protein
> (that means:
> ns_type: simple
> pbc=no
> rlist=0
> coulombtype=cut-off
> vdwtype=cut-off
> rcoulomb=o
> rvdw=0)
> I got the following error while grompping:
> 
> Non-cutoff electrostatics used, forcing full Hessian format.

try using a shifted function with a cut+off of 1.0 nm or so, that should 
enable the sparse matrix representation.
> 
> and,  of course, even with 2 Gb memory, the simulation won't start:
> 
> -------------------------------------------------------
> Program mdrun_d, VERSION 3.3
> Source code file: smalloc.c, line: 113
> 
> Fatal error:
> calloc for full_matrix (nelem=280629504, elsize=8, file minimize.c, line 1866)
> -------------------------------------------------------
> 
> "I'm Your Worst Nightmare" (Creep)
> : Cannot allocate memory
> 
> I'm wondering, is there any mean to overcome the problem (but trivially 
> expanding memory or NMAing on a subset, let's say CA's)? Does not the 3.3 
> version use sparse matrix representation?
> Maybe I should use cut-off's, but does this work in vacuum?
> Thanks again for attention.
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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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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