[gmx-users] trjconv to remove periodicity (KALP15 in DPPC tutorial)
bat.demoulin at gmail.com
Wed Jul 10 16:24:56 CEST 2013
For a system with several component in the membrane, I think that
InflateGRO 2 would be more appropriate. See
http://code.google.com/p/inflategro2/ for the code and the related
2013/7/10 Atila Petrosian <atila.petrosian at gmail.com>
> 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
> 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
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