[gmx-users] system not equilibrated
Gmx Niki
gmx_gmx_12 at yahoo.com
Wed Jan 9 09:41:09 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?
please guide me
tnx
Niki
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