[gmx-users] position restraints

[Mark Abraham]

gadies at fh.huji.ac.il wrote:
> 
> Hi,
> 
> I tried using no temperature coupling and no constraints, that did not 
> help.
> If I run the simulation without the position restraints it works OK.

OK, so they're (interacting with something else to be) generating a 
numerical problem.

> Could there by something wrong with the posre file (I'll attach it at 
> the end of the email).
> I want one of the atoms in the lipid to stay in one place and the rest 
> to wiggle around it. Is there any other way to do that which is not 
> position restraints.

After the fact, you could choose to translate any atom of your choice to 
a fixed point and the system with it, using (say) VMD. It wouldn't mean 
much of anything, apart from probably no longer being a simulation in an 
inertial reference frame.

Unless there's a meaningful purpose to seeing such a thing in a test 
run, it's really not worth anyone's time. If there is, then explaining 
it the first time makes you sound much more like someone with a real 
issue, than someone just trying to make something fit some preconception 
about pleasant appearance.

> Thanks Gadi
> 
> 
> [ position_restraints ]
> ; atom  type      fx      fy      fz
>      1     1  0  0  0
>      2     1  0  0  0
>      3     1  0  0  0
>      4     1  0  0  0
>      5     1  0  0  0
>      6     1  0  0  0
>      7     1  0  0  0
>      8     1  1000.0  1000.0  1000.0
>      9     1  0  0  0
>     10     1  0  0  0
>     11     1  0  0  0
>     12     1  0  0  0
>     13     1  0  0  0
>     14     1  0  0  0
>     15     1  0  0  0
>     16     1  0  0  0
>     17     1  0  0  0
>     18     1  0  0  0
>     19     1  0  0  0
>     20     1  0  0  0
>     21     1  0  0  0
>     22     1  0  0  0
>     23     1  0  0  0
>     24     1  0  0  0
>     25     1  0  0  0
>     26     1  0  0  0
>     27     1  0  0  0
>     28     1  0  0  0
>     29     1  0  0  0
>     30     1  0  0  0
>     31     1  0  0  0
>     32     1  0  0  0
>     33     1  0  0  0
>     34     1  0  0  0
>     35     1  0  0  0
>     36     1  0  0  0
>     37     1  0  0  0
>     38     1  0  0  0
>     39     1  0  0  0
>     40     1  0  0  0
>     41     1  0  0  0
>     42     1  0  0  0
>     43     1  0  0  0
>     44     1  0  0  0
>     45     1  0  0  0
>     46     1  0  0  0
>     47     1  0  0  0
>     48     1  0  0  0
>     49     1  0  0  0
>     50     1  0  0  0

That's probably fine if grompp doesn't complain - but you can delete all 
the position restraints with zero force, since they are doing nothing.

Mark