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

Ravasio Riccardo riccardo.ravasio at epfl.ch
Fri May 27 15:49:25 CEST 2016

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,


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