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

Nuno Ricardo Loureiro Ferreira nunolf at ci.uc.pt
Wed May 7 23:20:01 CEST 2003

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
Here goes the promptp output:
[nuno at thunderpiu apagar]$ g_msd_d -f ch3oh_equil.trr -s ch3oh_all.pdb -o



-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.

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

Phone: +351 239 852080
Fax: +351 239 827703

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