Rabab Toubar wrote:
Hi,
I set my .mdp file to minimize the system for 1000 steps, but it stopped
at ~200 saying: "Stepsize too small, or no change in energy.
Converged to machine precision, but not to the requested precision Fmax
< 10" but the molecule is now outside the box
This is not really a problem, provided that both the potential energy and Fmax
that resulted are
reasonable.http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
I did position restraint for 2ns using LINCS, and things went well
running md, it ran for only 0.3 ns out of 30, and I got an error message
that 1-4 interaction between 2 atoms are at a distance > table-size
(1nm) with a suggestion to increase the table-extension in mdp file.
I checked
http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off
suggesting reminimizing.
The other possibility is that your .mdp settings are inappropriate, but you
haven't provided that information.
My question is: is it OK that the system doesn't minimize till the end
of the specified number of steps? is it OK to be outside the box as long
as you assign boundary conditions as in case of NAMD? and what is the
best option - you think - I have to solve the md problem
Whether or not you need to revisit the EM procedure depends on how well it
actually did (see comment above). The periodicity effect is a non-issue, since
there is no "outside" of a periodic box.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
Any suggestions are highly apprecitaed
Rabab
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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