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

[Ravasio Riccardo]

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