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

[swati rana]

Hi Shine,

I have a query, before packing the lipids around the protein and ligand did
you restrain the whole system i.e protein and ligand and in the em.mdp file
is this vat you specified "define = -DSTRONG_POSRES".... Please let me
know.

Thanks in advance

Swati.


On Tue, Apr 9, 2013 at 4:50 PM, Anirban <reach.anirban.ghosh at gmail.com>wrote:

> 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
> >
> >
> >
> >
> >
> >
> > --
> > View this message in context:
> >
> http://gromacs.5086.x6.nabble.com/Lipid-membrane-partially-broken-and-create-huge-voids-after-NVT-tp5007128.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
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