[gmx-users] normal modes analysis

[Anton Feenstra]

Osmair Vital de Oliveira wrote:
> Hi
> 
> I tried performed calculation of  normal modes analysis:
> 
> g_nmeig -f nm.mtx -s xxx.gro -o -v
> 
> but the program complains that:
> 
> Reading frame       0 time    0.000   Dimensionality of matrix: 15360
> Fatal error: calloc for hess (nelem=235929600, elsize=4, file g_nmeig.c,
> line113): Cannot allocate memory

Unless you have 4*235929600 = about 1Gb of memory, you can't do this.
But, this means you are doing NM on 5120 atoms. Is that what you
really want & need? If this is e.g. a protein, you may want to limit
yourself to backbone, Ca's, or e.g. binding site. Also, even if you
have >1Gb of memory, diagonalizing this matrix (which is what g_nmeig
will do) will be extremely time-consuming.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|