Unlikely anything on top of dihedrals.
Try to use VMD to see if the lipid molecules look as you like.
I do not have to handle lipid isomer simulations, fortunately.
Dr. Vitaly V. Chaban
On Wed, Jul 2, 2014 at 7:33 PM, Venkat Reddy venkat...@gmail.com wrote:
Thank you Sir. Sorry for the late
Dear Sir,
I have measured the dihedral angles for both cis and trans conformations
using VMD. As expected, for cis isomer the dihedral angle was 0 and for
trans = 180. Expect this, I couldn't find any change between these isomers.
On Thu, Jul 3, 2014 at 3:07 PM, Dr. Vitaly Chaban
Thank you Sir. Sorry for the late reply. So, the changes like dihedral
angle for C8-C9=C10-C11 should be 180 instead of 0 in trans state. Are
there any other adjustments I should make to build the trans lipid isomer
topology from cis? Thank you for your valuable time and concern.
On Mon, Jun 16,
Dear all,
I want to simulate a membrane protein system. My membrane is composed of
DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC topology
from lipidbook website. Since DOPC and DEPC are isomers, can I use the
topology of DOPC for DEPC also?
Thank and regards
Venkat Reddy
Of course, no. You need to adjust your topology (force field?) to
distinguish between cis- and trans- states.
Dr. Vitaly V. Chaban
On Mon, Jun 16, 2014 at 11:03 AM, Venkat Reddy venkat...@gmail.com wrote:
Dear all,
I want to simulate a membrane protein system. My membrane is composed of
