[gmx-users] Re: g_msd : input files question (David)

[Nuno Ricardo Loureiro Ferreira]

Hello again

I tryed to compute msd with g_msd_d, but it gives me an error.
Also added my molecule (MEOH) and its atom masses to
/opt/gromacs-3.1.4/share/top/atommass.dat
Here goes the promptp output:
[nuno at thunderpiu apagar]$ g_msd_d -f ch3oh_equil.trr -s ch3oh_all.pdb -o
msd.xvg

...

------------------------------------------------------------

-f ch3oh_equil.trr Input Generic trajectory: xtc trr trj gro g96 pdb

-s ch3oh_all.pdb Input Structure+mass(db): tpr tpb tpa gro g96 pdb

-n index.ndx Input, Opt. Index file

-o msd.xvg Output xvgr/xmgr file

-mol diff_mol.xvg Output, Opt. xvgr/xmgr file

Option Type Value Description

------------------------------------------------------

...

WARNING: masses will be determined based on residue and atom names,

this can deviate from the real mass of the atom type

Opening library file /opt/gromacs-3.1.4/share/top/atommass.dat

Opening library file /opt/gromacs-3.1.4/share/top/aminoacids.dat

Group 0 ( System) has 221184 elements

Group 1 ( MEOH) has 221184 elements

Select a group: 0

trn version:

Fatal error: Float size 0. Maybe different CPU?



Any help will be appreciated

Nuno Ferreira

P.S. By the way, I don't use CHARMM because it's manual is not so
straightforward, that's why I'm using namd. Also I do not have any help from
the Harvard guys, only the MSI(accelerys) version, CHARMm, has it.



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Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal

Phone: +351 239 852080
Fax: +351 239 827703
www.biolchem.qui.uc.pt
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