[gmx-users] Re: Atoms are fused after inserting in membrane

[Justin Lemkul]

On 3/28/13 6:38 AM, Dr. Vitaly Chaban wrote:
>> Does that mean the atoms will shrink and adjust at the time inflategro step
>> and
>> this closely packed lipids will stay apart? Because as you said the energy
>> of course will be high on selected atoms during first EM step.
>> Could you suggest me that, can I proceed as such with my system, since there
>> is no problem in grompp and EM step (except high energy on some atom).
>
>
> The energy will normalize during molecular dynamics stage.
>

...assuming the energy is not so high as to cause an immediate crash :)

-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

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