[gmx-users] Re: system not equilibrated
sara_15_s at yahoo.com
Wed Jan 9 15:03:59 CET 2013
> 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.
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
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