[gmx-users] NMA problems with mass-weighting -m option

[Ravasio Riccardo]

Dear Tsjerk,

I forgot to mention that I also tried the option -nom, but in my eigenval.xvg file I have always the same text line with written "mass-weighted eigenvalues", and the eigenvectors are also the same. What is happening?

I thank you for your answer and help.

Bests,

Riccardo
________________________________________
De : gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> de la part de Tsjerk Wassenaar <tsjerkw at gmail.com>
Envoyé : samedi 28 mai 2016 20:08
À : Discussion list for GROMACS users
Objet : Re: [gmx-users] NMA problems with mass-weighting -m option

Hi Riccardo,

The boolean options are specified as -m or -nom, without further arguments.
For non-mass-weigthed you want -nom.

Hope it helps,

Tsjerk
On May 27, 2016 15:49, "Ravasio Riccardo" <riccardo.ravasio at epfl.ch> wrote:

> Dear gmx users,
>
>
> After performing Normal Mode Analysis, I would like to print a non
> mass-weighted spectrum, but both with option -m false and with -m true I
> get mass-weighted eigenvalues and eigenvectors. Why? I'm using version
> 5.1.2. I looked at the source code, but it was of version 3.2.0: maybe the
> -m option was forgotten in the last version? Or, what am I doing wrong?
>
>
> I'm using the usual following commands:
>
>
> gmx_d grompp -v -f nma.mdp -c $STRUCT-vacuum-min$((sample-1)).gro -p
> $STRUCT.top -o $STRUCT-vacuum-nma.tpr
>
>
> gmx_d mdrun -v -s $STRUCT-vacuum-nma.tpr -mtx $STRUCT-vacumm-nma.mtx
>
>
> gmx_d nmeig -f $STRUCT-vacumm-nma.mtx -s $STRUCT-vacuum-nma.tpr -m true
> -last 3693
>
>
> I tried to put also 0/1 or yes/no, but nothing changes.
>
>
> I thank you for your kindness and for your help.
>
>
> Best regards,
>
>
> Riccardo
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