On 12/10/12 3:48 PM, francesco oteri wrote:
Dear gromacs users,
I am facing a very tricky problem in building a stable topology.
In particular I am trying to use MARTINI force-field and I noticed that if
I use a box whose the side size is smaller than 20nm, the minimization
fails with this message:
Reading file 01em.tpr, VERSION 4.6-beta1 (single precision)
Starting 12 tMPI threads
Using 12 MPI threads
Making 2D domain decomposition 4 x 3 x 1
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 2000
Step= 14, Dmax= 1.2e-06 nm, Epot= 4.42099e+18 Fmax= inf, atom= 39063
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 1000 (whichmay not be possible for your system).
It stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 4.4209897e+18
Maximum force = inf on atom 39063
Norm of force = inf
With this information, you should be able to deduce the source of the problem.
gcq#142: "One Ripple At a Time" (Bianca's Smut Shack)
But, if I use a box bigger then 19.5nm the minimization, although with some
LINCS warning, succeeded!
These LINCS warnings will also give the same information as to where problems
start.
I found the problem with gromacs 4.5.5, 4.6beta1 and beta2.
I am attaching the script (crea_topo.csh) I am using to build the
topologies as well as all the input files you need to replicate the error.
The different topologies have been obtained changing the value of the
variable side in crea_topo.csh
How many values you have tried? What is the minimum box size necessary to
accommodate your system? This all seems like random failures from unstable
configurations.
As you can notice from the script, the structure is initially minimized in
vacuo to remove problems due in the all atoms-coarse grained transformation
and then it is solvated, Then, water molecules closer then 0.8nm to protein
are rmoved through vmd.
What was the outcome of the in vacuo minimization?
Can you give me some clue on how to solve the problem, except changing the
software?.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
-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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