[gmx-users] minimization

[Tsjerk Wassenaar]

Hi Morteza,

How did you obtain these structures? If they were modeled, maybe in
part, check for knots and chain overlaps. Also check whether you're
using PBC and if so, whether the box is large enough or you may have
overlapping periodic images.

Cheers,

Tsjerk

2009/8/13 Mark Abraham <Mark.Abraham at anu.edu.au>:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623