[gmx-users] Lipid membrane partially broken and create huge voids after NVT

[Anirban]

After NVT, usually the lipid bilayer move away from each other creating
some voids, which occurs due to absence of pressure coupling. But its not a
problem. You can go ahead and carry out NPT and see that bilayer has
settled to normal position.

-Anirban


On Tue, Apr 9, 2013 at 3:04 PM, sdshine <sdshine at gmail.com> wrote:

>  Gromacs users,
>
> 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
>
> ; position restraint file for DPPC P8
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    8    1       0       0       1000
> -------------------------------------------------------
>
> My topology has the last part...
> ----
> -------
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include lig topology
> #include "lig.itp"
>
> ; Strong position restraints for InflateGRO
> #ifdef STRONG_POSRES
> #include "DSTRONG_POSRES_B.itp"
> #endif
>
> ; Include DPPC topology
> #include "dppc.itp"
>
> ;strong position restraints for DPPC
> #ifdef POSRES_LIPID
> #include "DPOSRES_LIPID.itp"
> #endif
>
> ; Include water topology
> #include "spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> complex protein in water
>
> [ molecules ]
> ; Compound        #mols
> Protein_G       1
> Lig             1
> DPPC           125
> SOL             3199
> CL               35
> NA               39
> -----------------------------------
>
> 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.
>
> Thanks in advance
>
> -Shine
>
>
>
>
>
>
> --
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