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

[Justin Lemkul]

On 3/27/13 11:32 PM, sdshine wrote:
> Dear all,
>
> 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).
>
> or Do I need to manually remove those overlapping lipids and water
> molecules.
>

No, InflateGRO does this for you.  After inflation, there should be no water in 
the system and the lipids should have expanded outward.  Any that were too close 
(as defined by the cutoff specified on the command line) should have been deleted.

-Justin

-- 
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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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