[gmx-users] two problems with gromacs 4.5.3

[Roland Schulz]

On Mon, Nov 22, 2010 at 2:55 PM, Sanku M <msanku65 at yahoo.com> wrote:

> Hi,
>
> When using gromacs 4.5.3, I experienced two problems ( neither of which
> exist in gromacs 4.0.7 or older version like 3.3.3)
>   1. when issuing grompp command to start one of my  simulations, gromacs
> 4.5.3 gives me fatal error:
>       'can not find atom type SNa .'
>   However, with gromacs 4.0.7 and gromacs 3.3.3, for the  same simulation ,
> grompp runs smoothly ( as atom type SNa indeed exist in my directory).
> I am not sure what is wrong with grompp in gromacs 4.5.3
>

The folder layout for the input files has changed. Make sure you have the
files in the correct location for 4.5.3.

>
> 2. when using g_density command , after processing data , gromacs 4.5.3
> gives an error :
> *** glibc detected *** double free or corruption (out): 0x00000000006d8ce0
> ***
> Aborted
>
> But, the same g_density with gromacs 4.0.7 and gromacs 3.3.3 works
> smoothly.
>

That seems to be a problem in g_density. Please open a bug on
bugzilla.gromacs.org with enough detail to reproduce the error.

Roland


>
> Any idea  will be appreciated .
> Sanku
>
>
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