[gmx-users] Re: request

[David van der Spoel]

sina wrote:
>  
> Dear developers,
> I am a member of Computational Chemistry research group at university of 
> Tehran. In one of our recent projects, we needed software for executing 
> our MD calculations. In these respect, we chose GROMACS software because 
> of its great utilities in MD simulations. We’ve gotten source codes and 
> other related programs from www.gromacs.org and installed them 
> successfully. we also executed the GROMACS demo example (gmxdemo) 
> successfully, but, the version of software that was written in the 
> output files was gromacs.3.1.4 in despite of the fact that we had 
> installed the gromacs.3.3.1 version. Then, we tried to run the tutorial 
> examples. Although, for one of them (speptide) the process was 
> implemented successfully, but, for the other examples (water, methanol 
> and mixed) surprisingly we got the following error when we tried to 
> execute grompp –v command:
>  
> creating statusfile for 1 node...
>  
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> WARNING 1 [file grompp.mdp, line unknown]:
> Unknown left-hand init_step in parameter file
>  
> WARNING 2 [file grompp.mdp, line unknown]:
> Unknown left-hand nbfgscorr in parameter file
>  
> WARNING 3 [file grompp.mdp, line unknown]:
> Unknown left-hand nstcheckpoint in parameter file
>  
> WARNING 4 [file grompp.mdp, line unknown]:
> Unknown left-hand table-extension in parameter file
>  
> WARNING 5 [file grompp.mdp, line unknown]:
> Unknown left-hand gb_algorithm in parameter file
>  
> WARNING 6 [file grompp.mdp, line unknown]:
> Unknown left-hand nstgbradii in parameter file
>  
> WARNING 7 [file grompp.mdp, line unknown]:
> Unknown left-hand rgbradii in parameter file
>  
> WARNING 8 [file grompp.mdp, line unknown]:
> Unknown left-hand gb_saltconc in parameter file
>  
> WARNING 9 [file grompp.mdp, line unknown]:
> Unknown left-hand implicit_solvent in parameter file
>  
> WARNING 10 [file grompp.mdp, line unknown]:
> Unknown left-hand andersen_seed in parameter file
>  
> Fatal error: Too many warnings, grompp terminated
>  
> The version of software that we saw in the output log file of the 
> speptide example was gromacs.3.1.4 too. So we have two problems:
> a) we have installed the 3.3.1 version but in the output log files we 
> see 3.1.4.
> b) we can’t run” water”, “methanol” and “mixed” tutorial examples 
> because of the mentioned error and warnings that are appeared when we 
> run grompp –v.
> We searched the FAQ to solve the problem, but, we didn’t find any useful 
> comment.. I appreciate all of your notification and instructions.
>  
> Best Regards;
> Sina 
It seems that you have two version installed. You don't say which OS you 
use though, but please check the command
"which mdrun"
it will tell you which version you are using.

Plesea put further questions on the mailing list
>  
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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