[gmx-users] minimization

[Mark Abraham]

Morteza Khabiri wrote:
> Dear users
> 
> I have a dimer protein which I want to minimized it..unfortunately the
> protein is in high energy level and before starting to minimize it
> explode.
> I already went through users email and also wiki gromacs and also I tried
> all the way like changing time step, change coulomb type ,... but they did
> not work ......
> 
> As MARK suggest me I try to minimize monomer separately but the monomers
> itself also have high energy and it is not possible to minimize them...

OK, so simplify further to find the problem. Minimize just one half of a 
monomer, etc. Consider writing a script to run the minimization to make 
this process fast. Remember to look at the structures to identify 
obvious problems.

Mark

> I change the forcefield from olps to gromacs and minimization work. I did
> several minimization by gromacs forcefiled and then I tried to minimized
> the system by OPLS but again the system start exploiding...
> Is there any idea that why the minimization work by gromacs but not work
> with opls?????
> finally I should simulate my system by opls and if I want to do it my
> system still not minimized for OPLS....
> I will apprecite if there will be some idea for my problem
> 
> thanks
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