[gmx-users] enegry minimisation

[Erik Marklund]

sonali dhindwal skrev:
> Hello All
> This question may sound trivial to many, but as i am new to this 
> field, please help.
> I want to ask a question regarding my previous query of distortion of 
> protein strucutre after molecular dynamcs simulation.
> I have noticed that after enegry minimisation using steepest decent 
> algorithm, using emtol of 1000 kJ mol^-1 nm^-1 .
> So is it necessary to do enegry minimisation step before MD, because 
> this is my modeled protein, and i have  already done energy 
> minimisation using different program and after that I have done 
> refinement also.
> Thanks and regards
> ^
>
> --
> Sonali Dhindwal
>
>
That depends how that minimization was carried out. Did it use the same 
forcefield parameters and the same boxsize etc., then in principle no. 
If not, then I strongly suggest doing EM before MD to prevent problems 
later on.

I don't understand what it is that you noticed after energy minimization.

Cheers,

-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/