[gmx-users] TFE-water minimization

[Mark Abraham]

Owen, Michael wrote:
> 
> Hello,
> 
> I have created my own TFE.itp file for a mixed solvent simulation 
> containing TFE and TIP4P water.  To test my TFE file I put one TFE 
> molecule in a box of solvent and and tried to minimize it using the 
> following parameters:
> 
> 
> define              =  -DPOSRES
> cpp                 =  /lib/cpp
> ;constraints         =  all-bonds
> integrator          =  steep
> nsteps              =  2000
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  0.05
> emstep              =  0.01
> nstcgsteep            =  1000
> nstcomm             =  1
> ns_type             =  grid
> ;deltagrid           =  2
> rlist               = 1.4
> rcoulomb            = 1.4
> rvdw                = 1.4
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
> lincs_iter          =  4       

That's all fine.

> Can you tell me what I can do to solve this problem? 

Check your topology. Look at your before-and-after structures.

Mark