[gmx-users] restraints on water oxygen atoms

[Justin Lemkul]

On 6/10/13 3:37 AM, Shima Arasteh wrote:
> Thanks for your reply.
>
> The system I am trying to equilibrate is composed of popc/ peptide/ions/water. I built the system by InflateGRO methodology as you wrote in kalp-dppc tutorial. The last gro file which gave me the acceptable APL, was used as the starting configuration in next steps. But before going on, I found some overlaps between lipids acyl chains and peptide structure. So tried to move the  lipid residues caused the overlaps. Then there are some gaps between peptide and near lipid chains. As a result, I see the water cleavage in these regions.
> Would you please give me any suggestions? How would I make a better packed system without disturbing overlaps or crashes?
> Would you please help me?
>

Don't manually delete lipids.  InflateGRO overestimates APL, so if you reach 
your target value, realize that the lipids are more packed than that and the 
true APL is much smaller.  I discuss that fact in the KALP-DPPC tutorial.  I 
generally stop packing when the lipids claim to be about 10% higher than the 
desired APL.  If you delete lipids because you've forced them together too much, 
then you're going to severely compromise the membrane.

-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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