[gmx-users] Regarding lipid topology

[Dr. Vitaly Chaban]

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 <venkat4bt at gmail.com> wrote:
> 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, 2014 at 4:44 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
> wrote:
>
>> 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 <venkat4bt at gmail.com>
>> wrote:
>> > 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 Chirasani
>> > PhD student
>> > Laboratory of Computational Biophysics
>> > Department of Biotechnology
>> > IIT Madras
>> > Chennai
>> > INDIA-600036
>> > --
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>
>
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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