[gmx-users] ngmx doesnot work; CH3-CH2-OH

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 31 01:34:57 CET 2011

gromacs wrote:
> Hi Everyone,
> Program ngmx, VERSION 4.0.7
> Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708
> Fatal error:
> reading tpx file (md1.tpr) version 73 with version 58 program
> I installed 4.0.7 before, and now i installed 4.5.3. How can i use ngmx now?

You need a compatible .tpr file, i.e. one generated with version 4.5.3, 
otherwise you have to use a 4.0.7 .tpr file with the 4.0.7 version of ngmx. 
Higher versions can read older file formats, but the reverse is generally not true.

>  The second question is running C2H5OH (ethanol). It should be 9 atoms 
> per molecule. But i download the .top using PRDUG, the C2H5OH has 4 
> atoms. So i can still run, but some H atoms are ingored. Is it still no 
> problem?

PRODRG produces united-atom topologies for the Gromos96 force fields.  If you 
need or want a different force field, you need to build a suitable topology by 
some other method.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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