Hi all,
I have a question of surface tension in membrane simulation. I found that in
equilibration and production step, the pressure set up for membrane simulation
is below:
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype =
not tell apart the last peptide atom and
the first lipid atom. Could you please let me know how to solve this problem?
Thanks a lot!
Best,
Ning
On Wednesday, August 27, 2014 10:23 AM, Justin Lemkul jalem...@vt.edu wrote:
On 8/27/14, 10:14 AM, Xiang Ning wrote:
Hi all,
I was trying to put
yes 1.0 1.0'
Found a second defaults directive.
I would like to know, how can I combine the itp files into one correct top
file?
Thank you very much!
Best regards,
Ning
On Wednesday, August 27, 2014 11:41 AM, Xiang Ning xiang_n...@yahoo.com wrote:
Dear Justin,
Sorry I
Lemkul jalem...@vt.edu wrote:
On 8/24/14, 4:36 PM, Xiang Ning wrote:
Dear Justin,
Thanks for your help! It did work when I use grompp to generate tpr file.
However, after obtaining em.tpr file, I want energy minimization of the
membrane+water+ion system, so I typed mdrun -v -deffnm em
, Xiang Ning wrote:
Hi All,
I am using POPC/POPG mixed membrane built by Charmm-gui. After remove ions
and water from CHARMMGUI pdb and save just the membrane pdb, and use this pdb
with pdb2gmx to get top file (I used charmm36), then I would like to know,
how to add water and ions back
Hi All,
I am using POPC/POPG mixed membrane built by Charmm-gui. After remove ions and
water from CHARMMGUI pdb and save just the membrane pdb, and use this pdb with
pdb2gmx to get top file (I used charmm36), then I would like to know, how to
add water and ions back to the system? I read the
