[gmx-users] Error when try obtain protein energies instead of system energies

[Mark Abraham]

On 22/11/2011 3:34 PM, Rodrigo Faccioli wrote:
> I believe I understood my mistake. In my compute_energy.mdp file, the 
> value of nstep was zero. However, it is necessary to  set to 1.

Yes, but that does not affect the system-size mismatch between run input 
file and trajectory file.

Mark

>
> I'll make others testes to evaluate my changes.
>
>
> --
> Rodrigo Antonio Faccioli
> Ph.D Student in Electrical Engineering
> University of Sao Paulo - USP
> Engineering School of Sao Carlos - EESC
> Department of Electrical Engineering - SEL
> Intelligent System in Structure Bioinformatics
> http://laips.sel.eesc.usp.br
> Phone: 55 (16) 3373-9366 Ext 229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
>
>
> On Tue, Nov 22, 2011 at 1:34 AM, Dallas Warren 
> <Dallas.Warren at monash.edu <mailto:Dallas.Warren at monash.edu>> wrote:
>
>     The error message is stating that your .trr file only has 390
>     atoms in it, where as the .tpr file has 20524.  Those need to match.
>
>     Where you have made the error, tried to see it, but with all the
>     full paths in your command lines makes it difficult to see what
>     the actually commands are.  Look at the step where you generated
>     those two files, that is likely to be where the issue is.
>
>     Catch ya,
>
>     Dr. Dallas Warren
>
>     Medicinal Chemistry and Drug Action
>
>     Monash Institute of Pharmaceutical Sciences, Monash University
>     381 Royal Parade, Parkville VIC 3010
>     dallas.warren at monash.edu <mailto:dallas.warren at monash.edu>
>
>     +61 3 9903 9304 <tel:%2B61%203%209903%209304>
>     ---------------------------------
>     When the only tool you own is a hammer, every problem begins to
>     resemble a nail.
>
>
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