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

Dear Justin I do your tutorial entitled KALP15 in DPPC . In Step Three: Defining the Unit Cell Adding Solvent, You said Use trjconv to remove periodicity . When I use trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact, gromacs tell me: Select group for output. Which

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

On 7/10/13 8:32 AM, Atila Petrosian wrote: Dear Justin I do your tutorial entitled KALP15 in DPPC . In Step Three: Defining the Unit Cell Adding Solvent, You said Use trjconv to remove periodicity . When I use trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact,

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

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

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

Hi, 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 publication http://pubs.acs.org/doi/full/10.1021/ci3000453 Bests, Baptiste 2013/7/10 Atila Petrosian

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

Dear Baptiste Very thanks for your reply. Unfortunately, I have not access to InflateGro2. I encountered with error. If there are a script for InflateGro2 like InflateGro. please sent me perl script related to InflateGro2. Best wishes. -- gmx-users mailing listgmx-users@gromacs.org

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

On 7/10/13 10:46 AM, Atila Petrosian wrote: Dear Baptiste Very thanks for your reply. Unfortunately, I have not access to InflateGro2. I encountered with error. If there are a script for InflateGro2 like InflateGro. please sent me perl script related to InflateGro2. It's freely available