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

[chris.neale at utoronto.ca]

>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 GPCR,
>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.