Re: [gmx-users] tilt angle for POPC

Thanks, I agree. I will do as you recommended. Cheers, Mohsen On Fri, Jan 19, 2018 at 9:23 AM, Justin Lemkul wrote: > > > On 1/19/18 11:16 AM, Mohsen Ramezanpour wrote: > >> On Fri, Jan 19, 2018 at 5:55 AM, Justin Lemkul wrote: >> >> >>> On 1/18/18 1:28 PM, Mohsen Ramezanpour wrote: >>> >>> Hi

Re: [gmx-users] tilt angle for POPC

On 1/19/18 11:16 AM, Mohsen Ramezanpour wrote: On Fri, Jan 19, 2018 at 5:55 AM, Justin Lemkul wrote: On 1/18/18 1:28 PM, Mohsen Ramezanpour wrote: Hi Justin, On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: Dear Gromacs users, I a

Re: [gmx-users] tilt angle for POPC

On Fri, Jan 19, 2018 at 5:55 AM, Justin Lemkul wrote: > > > On 1/18/18 1:28 PM, Mohsen Ramezanpour wrote: > >> Hi Justin, >> >> On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: >> >> >>> On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: >>> >>> Dear Gromacs users, I am interested in

Re: [gmx-users] tilt angle for POPC

On 1/18/18 2:44 PM, Mohsen Ramezanpour wrote: I did more tests and here are the conclusions for the pick mentioned earlier. The pick appears when the -binw gets smaller and smaller. For the default value of gangle (which is 1), one cannot detect such a pick and you will get a normal distributi

Re: [gmx-users] tilt angle for POPC

On 1/18/18 1:28 PM, Mohsen Ramezanpour wrote: Hi Justin, On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: Dear Gromacs users, I am interested in calculation of tilt angle for the POPC headgroup (angle distribution between the P-N vecto

Re: [gmx-users] tilt angle for POPC

I did more tests and here are the conclusions for the pick mentioned earlier. The pick appears when the -binw gets smaller and smaller. For the default value of gangle (which is 1), one cannot detect such a pick and you will get a normal distribution. Even for a -binw of 0.1 everything looks fine.

Re: [gmx-users] tilt angle for POPC

Looking at index file made in the above mentioned way, as way as the following way: gmx make_ndx -f SYSTEM.gro -o index.ndx keep 0 r 1-100 name 1 upperleaflet 1 & a P N name 2 vector q gave the same results. Interestingly, even if I make the index file like: gmx make_ndx -f SYSTEM.gro -o index.

Re: [gmx-users] tilt angle for POPC

And, I used Charmm36 FF for simulations in Gromacs v. 2016.3 Cheers, Mohsen On Thu, Jan 18, 2018 at 11:28 AM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Justin, > > On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: > >> >> >> On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote

Re: [gmx-users] tilt angle for POPC

Hi Justin, On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: > > > On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: > >> Dear Gromacs users, >> >> I am interested in calculation of tilt angle for the POPC headgroup (angle >> distribution between the P-N vector and Z axis). >> I am not sure if

Re: [gmx-users] tilt angle for POPC

On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: Dear Gromacs users, I am interested in calculation of tilt angle for the POPC headgroup (angle distribution between the P-N vector and Z axis). I am not sure if my approach is correct as my angle distribution does not seem reasonable. Given a bil

[gmx-users] tilt angle for POPC

Dear Gromacs users, I am interested in calculation of tilt angle for the POPC headgroup (angle distribution between the P-N vector and Z axis). I am not sure if my approach is correct as my angle distribution does not seem reasonable. Given a bilayer with 200 lipids (100 lipids in each leaflet wi