[gmx-users] emtol

[Ghermes Chilov]

NHP> On Fri, 17 Jan 2003, [iso-8859-1] Tanos C. C. Franзa wrote:

>> 
>>       Hi folks,
>> 
>>       What is considered a suitable tolerance (emtol) for a energy minimization
>> of a big dimeric protein  (884 residues) in a water box  ?  In the article
>> cited bellow, Berendsen said that he performed an em with steepest descent
>> until a tolerance of 0,01 Kj/mol.nm. How to do this ? In my machine the most
>> I achieved was 1000 Kj/mol.nm in a water box. The calculation always stops
>> when the Fmax is about 1000 and gives me the following mesage: "Step size
>> too small. Converged to machine precision". What does it means ?
>> 

NHP> I usually perform em for systems of protein and water and I can reach to
NHP> Fmax = 0.001 using cg with emstep = 10^{-6} and double precision. Usually
NHP> the annealing simulations are done and then the em are performed for the
NHP> obtained configurations.

NHP> Phuong

Do you use any position restrictions? If it so, than you can make your
restriction potential more 'soft' - this could help in relaxing
complex systems (water + smt. else).

When you have solvated protein, you could first relax water with freezed
protein, and than relax the hole system.

Be careful with annealing - it may lead your structure too far from
PDB!

Luck!

Ghermes
Moscow State University