[gmx-users] Re: system not equilibrated

[sara azhari]

 > 
> 
> Hi all, 
> I ran energy minimization (em) step, (protein-CNT in water) by these conditions: 
> title        = Minimization 
> integrator    = steep 
> emtol        = 1000.0 
> emstep      = 0.01 
> nsteps        = 150000 
> energygrps    = Protein CNT 
>   nstlist        = 1 
> ns_type        = grid 
> rlist        = 1.0 
> coulombtype    = PME 
> rcoulomb    = 1.0 
> rvdw        = 1.0 
> pbc            = xyz 
> 
> 
> but when it recieves to 40000 step (nearly), it gives error: 
> 
> Step=  125, Dmax= 7.8e-06 nm, Epot= -1.79432e+07 Fmax= 8.35837e+04, atom= 10656 
> Step=  129, Dmax= 1.2e-06 nm, Epot= -1.79432e+07 Fmax= 8.35979e+04, atom= 10656 
> Stepsize too small, or no change in energy. 
> Converged to machine precision, 
> but not to the requested precision Fmax < 1000 
> 
> Double precision normally gives you higher accuracy. 
> 
> writing lowest energy coordinates. 
> 
> Back Off! I just backed up em2.gro to ./#em2.gro.1# 
> 
> Steepest Descents converged to machine precision in 130 steps, 
> but did not reach the requested Fmax < 1000. 
> Potential Energy  = -1.7943236e+07 
> Maximum force     =  8.3583656e+04 on atom 10656 
> Norm of force     =  2.1333945e+03 
> 
> then I ran my system with emtol=10 , but the error repeated too. then I ran it by double-precision , but was not successful too. 
> 
> 1- I changed fmax value only in .mdp file, is it correct? or I should change any parameter in topology file? 
> 2- is the nsteps too much ?and problem is long time?what is its problem? 

________________________________

You have a maximum force on the order of 10^4, which is an order of magnitude 
higher than what you initially requested.  mdrun is telling you that the problem 
is focused on atom 10656.  Open up your structure in your visualization software 
of choice and find that atom.  You likely have some unresolved clashes there 
that are causing this problem. 

justin
Dear Justin 

first, I get error on atom  number XXXX. after change emtol to 10 , I get same error on atom number YYYY. what' your idea? how to solve it? I use this file for PR step , but I get this error:  A charge group moved too far between two domain decomposition your system might be not equilibrated well enough my system without charge (total charge is zero) what' your idea? thanks