[gmx-users] distance restrained energy minimisation

[Mark Abraham]

jayant james wrote:
> Hi!
> I am attempting DISRES energy minimization. I'd like to turn ur 
> attention to the 2nd & 5th line below. these contain a common atom 2711 
> and the distance in the PDB file to its counterpart (2444 or 2575) is 55 
> angstroms well within the specified range. 

See manual section 2.2 entitled "MD Units" :-)

> But still I get a system 
> explode warning!!! The distances given is between SG of CYS to another 
> SG of a Cys. I suppose GMX is pushing/pulling  and the SG comes off!!!!

You're probably right.

> ;       ai      aj      type    index   type'   low     up1     up2     fac
>        2575    2620     1       1       1       60      60.1    85      1.0
>        2575    2711     1       2       1       40      40       70      1.0
> ;      2575    2824     1       3       1       40      40.1    60      1.0
>        2444    2620     1       4       1       62      62.05  100.00   1.0
>        2444    2711     1       5       1       40       40.1    80      1.0
> ;      2444    2824     1       6       1       47      47.1    57      1.0
> ~

Mark