[gmx-users] necessity of energy minimization

[Justin Lemkul]

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

========================================