[gmx-users] Re: Simulation problem with extended membrane system!

liu xin zgxjlx at gmail.com
Wed Sep 13 05:39:45 CEST 2006

If I solvate my GPCR into the DPPC128 system using genbox, there are only
about 50 lipids left, which I think are too few, so I want a larger starting

According to your note, when I did step 3, loaded my DPPC183 system to VMD,
I found the edges lined up poorly, there is are gaps between two periodic
cells. I also try other system like DPPC200, DPPC150, but only the original
dppc128 system, I've equilibrated it for 2ns,  have no  gap between two
periodic cells.

So, I will try another starting structure, like POPC, DMPC or your POPE. But
I still can't figure out why there are gaps when using genbox to extend the
DPPC system.

On 9/9/06, chris.neale at utoronto.ca <chris.neale at utoronto.ca> wrote:
> >According to your suggestion, I did a energy minimization and then a MDS
> >with "freezegrps=SOL, freezedim=N, N, Y", the rest of the system were
> >simulated with no constraint. This time I use semiisotropic pressure
> >coupling with tau_p=5. The system will be equilibrated with water
> >constrained for 1ns, do you think it's enough?
> It will be more than enough. Use vmd to watch the trajectory. It's
> important
> actually look at the structures.
> >The reason why I want to extend the system is because that I've got a
> >and I want to simulate it in a DPPC membrane environment, but the z
> >dimension of the membrane, downloaded from Dr. Tielman's websit,  was not
> >large enough, when I align the protein to the z axis of the membrane I
> find
> >the two ends of the protein are poking out of both water layers.
> In this case you may not need to extend the lipid. Why not just use
> editconf to
> increase the z dimension while keeping the x and y constant. Then insert
> your
> protein, re-solvate, re-equilibrate, and your into production. If your
> lipid
> takes up a maximum amout of space D in the xy-plane, then x and y need
> only be
> equal to [D + 2*max(LJ cutoff, Coulombic real-space cutoff) + some extra
> amount
> in case the protein fluctuations make it larger during the simulation].
> >Back to the previous question, after solvate the lipids in water, can I
> >remove the water placed in the membrane with excel instead of script?
> Cause
> >with editconf we can know the z dimension of the lipids_only system,
> let's
> >say 6, so if I center the whole system with 0 0 0, the water molecules
> with
> >z coordinates below 3 and above -3 will be excluded. If I'm right, I
> think
> >excel can do it too, or the scripts have some advantages?
> Sure you can use excel, but I am not sure how that is going to affect your
> formatting or how gromacs responds to formatting (i.e. spaces / tabs / the
> number of each) So scrips have 2 advantages: 1)formatting is easily
> maintained,
> 2)if you need to do it a second time you just type one command. After
> using
> excel (or a script) make sure to update you topology file to indicate the
> number
> of waters.
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