[gmx-users] Re: Lipid membrane partially broken and create huge voids

Dr. Vitaly Chaban vvchaban at gmail.com
Tue Apr 9 12:16:14 CEST 2013

> My complex heterogenous system has DPPC+ Protein+ligand. I have packed
> lipids around protein and ligand using Inflategro method, (APL: 0.79 nm2
> got
> after 24th iteration) followed by adding solvent and neutralize the system
> by adding CL35 & NA 39, since my system has -3.999 non zero total charge.
> Then the minimized system has the energy -2.8989 with Max force= 9.58
> converged normally in step 464 step.
> I used lipid constraints in the file "DPOSRES_LIPID.itp" before NVT
> There is no grompp error and no problem till NVT, after this
> equillibration,
> half of the DPPC along with SOL is no showing in VMD. Could any suggestions
> on this behavior.

I think your particles are still there...

Try to adjust VMD settings.

Dr. Vitaly Chaban

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