On 1/9/13 3:41 AM, Gmx Niki wrote:
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= 15
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 4 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
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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