On 1/10/13 2:32 AM, Gmx Niki wrote:
Hi All,
when I run energy minimization the system gives error, and broke up. it has error about
steep integrator and says tha: "steepest time is too small".
It's always better to post the full message you get, rather than leaving us
guessing what you're dealing with. In this case, I'm assuming what you're
seeing is
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,
which is not actually an error. I don't know what you mean by "broke up," but
maybe PBC effects explain it.
but the system is running by MD integrator without any em step). is the energy
minimization necessary to all cases? for example in DL_POL software we dont
have enegy minimization , seperately. is it correct that I start simulation
steps by md integrator and NVT ensemble?
EM is always recommended. In the majority of cases, if you try to go straight
into dynamics, the system will explode due to high forces. You might get lucky
and not need it, but that would be extremely uncommon.
-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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