ABEL Stephane 175950 wrote:
Hi all,
I have simulated a system containing 55 DPC molecules, a peptide some ions
and water in a cubic box. Initially all molecules were placed randomly in the
box. As expected during the simulation all the DPC molecules aggregate to
form a stable micelle with the peptide located at the micelle interface.
Now I would like to plot some MD configs in a PDB format some configs where
the micelle and the peptide are placed in the center of the box. To take into
account the PBC and to obtain the PDB, for the last frame at 150 ns as I used
trjconv with the following commands:
1- trjconv_mpi -f traj_KTM17_DPC_all.xtc -s hMRP1_K-TM17_DPC.tpr -pbc nojump
-b 150000 -e 150000 -o traj_KTM17_DPC_0ns_noJump.pdb
With "non-SOL" (DPC and peptide) as a group for output and where
traj_KTM17_DPC_all.xtc is the trajectory with *no* PBC transformation
2- trjconv_mpi -f traj_KTM17_DPC_0ns_noJump.pdb -s hMRP1_K-TM17_dpc.gro
-center -o traj_KTM17_DPC_0ns_noJump_center.pdb
With DPC as a group for centering and "System" (DPC and peptide) as a group
for output. the *.gro file contains only the DPC and peptide.
Unfortunately, these commands do not work since the micelle (and the peptide)
are not in the box center. I have tried many others commands with -pbc as
mol, res with no success.
I have never had much success using multi-molecule groups for centering or other
correction using trjconv. Centering on the peptide, i.e. trjconv -pbc mol -ur
compact -center, should do the trick. I have never found -pbc nojump to work
very well, for a reason that is still unknown to me.
-Justin
I used GMX version 4.0.7
Any advices would be helpful.
Stefane
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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