[gmx-users] using atom id to specify the position_restraints

[Binbin Liu]

Dear all,

I have two questions.
1. Is it possible to partially freeze pariticular ions during the energy 
minimisation?
2. Persumbly the answer to question 1 is yes. I use position_restraints in 
.top to freeze ions. Grompp gives warning:
fatal error: Atom index (69338) in position_restraints out of bounds (1-1)

What I have to done to try to solve this problem is: I change the order of 
topol_A.itp, ions.itp, spc.itp and [ position_restraints ] in .top. 
Unfortunately, neither does work. 

First, I put all .itp files on the top of.top followed by [ position_restraint 
] for protein, ions, and 2 waters. It looks like:
#include "protein.itp"
#include "ions.itp"
#include "spc.itp"
[ position_restraints ]
etc...

 GROMPP gives the above fatal error when it read to the atom id of ions 69338. 

Secondly, I put each .itp before the corresponding [ position_restraints ]. On 
the other word, it looks like :
# include "protein.itp"
[position_restraints ]
#include "ions.itp"
[position_restriants]
It still doesnt work.

Please, help is very appreciated.

Best,
Binbin