[gmx-users] trjconv to remove periodicity (KALP15 in DPPC tutorial)

[Atila Petrosian]

Dear Justin

Thanks for your quick reply.


I want to study a system containing DOPC and cholesterol and drug.

I correctly prepared gro files and topology parameters for this system.

I did previous step (Step Two: Modify the Topology) without problem.

I have 2 problems.

1) After I use trjconv -s em.tpr -f dopc_chol.gro -o dppc_chol_whole.gro
-pbc mol -ur compact,

When I see dppc_chol_whole.gro using vmd, almost 5 DOPC emerg lipid
structure.


2) In your tutorial, system contains DPPC and KALP and you used:

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

But in my case, system  contains DOPC and cholesterol and drug.

How to do these steps (Scale and shrink the lipid positions)?


Best wishes