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

[David]

On Wed, 2003-05-07 at 23:08, Nuno Ricardo Loureiro Ferreira wrote:
> 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?
> 
Do you really have 221184 atoms of methanol?

Are you sure the trr is OK? (use gmxcheck or something like that)
> 
> 
> 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
> Portugal
> 
> Phone: +351 239 852080
> Fax: +351 239 827703
> www.biolchem.qui.uc.pt
> ####
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel
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