[gmx-users] Density of States syntax question

[Chapman, Christopher W.]

Hi,

Per your suggestion, I uninstalled Gromacs v5.1.2, and installed Gromacs v5.0.1, and re-ran the tutorial (changing from TIP4PEW to TIP4P for simplicity). The tutorial ran fine, but when I tried calculating the dos, I get the following error message:

-------------------------------------------------------
Program gmx, VERSION 5.0.1
Source code file: /home/chaps/Work/gromacs/gromacs-5.0.1/src/gromacs/fft/fft_fftw3.cpp, line: 309

Fatal error:
Error initializing FFTW3 plan.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

I didn't notice any errors regarding fftw3 when I was installing this version of Gromacs (I followed the 'quick and dirty installation' from http://www.gromacs.org/Documentation/Installation_Instructions_5.0). I didn't think I needed any pre-requisite libraries, as I thought gromacs would install any necessary fftw libraries. Is this assumption wrong, or is there something else wrong here?

Thanks,

Chris

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Marcelo Depólo
Sent: Tuesday, May 31, 2016 10:04
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Density of States syntax question

Hi!

That's an bug that was not corrected yet for the 5.1 version. Its somehow linked to a safety measure that went nuts. The issue was already directed to the admins.

Try to use 501 version. For me, it works just fine.

Cheers!

2016-05-31 10:59 GMT-03:00 Chapman, Christopher W. <chapmancw at ornl.gov>:

> Hello all,
>
> I am new to Gromacs, so I apologize if this is a trivial question. I'm 
> running a Gromacs tutorial (found at
> https://github.com/wesbarnett/gromacs-tutorials/tree/master/1_tip4pew_
> water) using Gromacs v5.1.2, and I was trying to get the Density of 
> States from the production run. When I type in the following:
>
> gmx dos -f prd.cpt -s prd.tpr
>
> and choose any of the Groups listed (0 for 'System', 1 for 'Water', 2 
> for 'SOL'), I get the following:
>
> Program gmx dos, VERSION 5.1.2
> Source code file:
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/gmxana/gmx_dos.c, 
> line: 94
>
> Fatal error:
> Index contains atom numbers larger than the topology For more 
> information and tips for troubleshooting, please check the GROMACS 
> website at http://www.gromacs.org/Documentation/Errors
>
> What exactly does this mean, and how do I go about fixing this 
> (assuming it's possible)? Also, is it possible to get the density of 
> states for each individual atom (Oxygen and Hydrogen, in this case), 
> or is it only available for the molecule as a whole?
>
> Sincerely,
>
> Chris W. Chapman
> Computational Reactor and Medical Physics Group Nuclear and 
> Radiological Engineering Georgia Institute of Technology
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--
--
Marcelo Depólo Polêto
MSc Cell and Molecular Biology - UFRGS (Brazil) Group of Structural Bioinformatics - Room 202 Center of Biotechnology - UFRGS
Phone: + 55 51 3308-7770
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