Gromacs freeze proplems

User discussions
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1

GROMACS version:VERSION 4.5.5
GROMACS modification: No
Hi Gromacs users,

I am having a fatal error with the freeze groups function. What I want to do is make a water molecule (atom 145-148 ) free to move, and freeze all the rest.

in my .ndx file
[ fzgp1 ]
1 2 3 …
16 …144
[ fzgp2 ]
149 …
…31168
[ Ion ]
31169 …
…31568

in my .mdp file
…
freezegrps = fzgp1 fzgp2 Ion
freezedim = Y Y Y Y Y Y Y Y Y

in my .top file
#include “/home/b06504051/hsin/hsin/7792200200/ffnonbonded.itp”
#include “atomtypes.itp”
#include “tip4p_Ice.itp”
#include “Na.itp”
#include “Cl.itp”
#include “frz.ndx”

[system]
7792200200

[molecules]
H2O 7792
Na 200
Cl 200

After running the following command
gmx grompp -f 1.min.mdp -c naclsolution.g96 -r naclsoluiton.g96 -n frz.ndx -p topol.top -po 1.minout.mdp -o 1.min.tpr

and it shows a fatal error
ERROR 1 [file index_0420_1.ndx, line 1]:
Invalid directive fzgp1

I am not sure where the problem is. Do anyone have any suggestions?

2

Hi,

Removing the inclusion of index file (#include “frz.ndx”) from the top file should solve the error. Index files are input with the option -n to gmx grompp

\Alessandra

3

It works!!!
Thank you very much.