[gmx-users] dcd to gro!

Swetha Vijayakrishan swetha at www.cdfd.org.in
Tue May 20 07:20:01 CEST 2003

hi gromacs users,

i ran an MD simulation with the Charmm software.This simulation was run on
the HP Alphaserver ES-45 ( Compaq Alpha ).
I then converted the dcd file obtainded, to the trr format by using the
Trio software , which is a part of the MDtools package of the univ of
illinois,urbana campaign.
Now i tried using this converted trr file for analysis in gromacs.
when i tried the g_rms command i.e

g_rms -s x.pdb -f x.trr -o rmsd.xvg

i got the following error:

Warning: can not make broken molecules whole without a run input file,
         don't worry, mdrun doesn't write broken molecules

trn version:
Fatal error: Float size -1092145. Maybe different CPU?

Is it vecause i ran the simualtion on a different OS (true64 OS) and i'm
now viewing it on another(Red Hat 8.0 ,Linux).can u please tell me how do
i make it compatible in my machine(Red Hat 8.0,Linux) from where i need
to do the analysis.

Thanks and Regards



Swetha Vijayakrishnan

Project Assistant
C/O Dr.Shekhar.C.Mande
Centre for DNA Fingerprinting and Diagnostics(CDFD),
ECIL Road,Nacharam,
Hyderabad - 500076

Phone:: Direct: 91-040-7171442
        Indirect: 91-040-7151344/46/47/56 (lab extn 1400)

Fax  :: 91-040-(7155479-7155610>

Email:: swetha at cdfd.org.in
        swethasenorita at yahoo.com

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