[gmx-users] Energy minimizations with gmx3.2

[Alan Wilter Sousa da Silva]

But Marc and All, how is your ramachandran plot after such optimisation?

I mean, If we do too much EM our structures (according to procheck) get 
worse and worse.  Compare rama from your original PDB to your optimised 
(emtol < 1 or even <10).

I still prefer emtol = 100.  For instance, a PR-HIV down form 95% (rama 
PDB) to ~90% (rama optimised) in less 1500 steps with emtol = 100.

Cheers,
Alan

Marc Vogt wrote:
> No problem.  I currently use the GROMOS96 43a2 Forcefield. 
> 
> Marc
> 
> 
>>Thanks Marc,
>>
>>Just one thing else, which FF do you use?
>>
>>Marc Vogt wrote:
>>
>>
>>>Sure:
>>>
>>>title               =  mitwasser
>>>cpp                 =  /lib/cpp
>>>define              =  -DFLEXIBLE
>>>constraints         =  none
>>>integrator          =  l-bfgs
>>>dt                  =  0.002    ; ps !
>>>nsteps              =  10000
>>>nstlist             =  10
>>>ns_type             =  grid
>>>coulombtype         = Switch
>>>vdw-type            = Switch
>>>rlist               =  1.0
>>>rcoulomb            =  1.0
>>>rvdw                =  1.0
>>>;
>>>;       Energy minimizing stuff
>>>;
>>>emtol               =  10.0
>>>emstep              =  0.01
>>>epsilon_r           = 1
>>>
>>>
>>>Apparently you should be able to use emtol = 1.0, but I start to get
>>>problems converging to lower than 10.0 with my system.  
>>>
>>>hope this helps,
>>>
>>>Marc
>>>
>>
>>
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-- 
--------------------------
Alan Wilter Sousa da Silva
--------------------------
D.Sc. - IBCCF/UFRJ
Bolsista Pesquisador LAC-INPE
São José dos Campos (SP), Brasil
www.lac.inpe.br/~alan