Re: [gmx-users] Order Parameter for HII phase

2017-10-24 Thread Mohsen Ramezanpour
, Feb 23, 2017 at 8:08 AM, Piggot T. >>>>>> wrote: >>>>>> >>>>>> Hi, >>>>>>> >>>>>>> I don't believe this Chau paper is for deuterium order parameters >>>>>>> (as I >>>>>>>

Re: [gmx-users] Order Parameter for HII phase

2017-10-18 Thread Mohsen Ramezanpour
rameters and you can find more >>>>>> details >>>>>> in the papers referenced therein (e.g. the Douliez et al. and the >>>>>> Seelig et >>>>>> al. papers in particular). >>>>>> >>>>>> For unite

Re: [gmx-users] Order Parameter for HII phase

2017-02-23 Thread Mohsen Ramezanpour
performed in gmx order using the "SCD = (2/3) Sxx + (1/3) Syy" >>>>> equation >>>>> (which is nicely derived in the 1998 Douliez paper: >>>>> http://aip.scitation.org/doi/pdf/10.1063/1.476823) . The calculation >>>>> requires an a

Re: [gmx-users] Order Parameter for HII phase

2017-02-23 Thread Antonio Baptista
llist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 23 February 2017 12:16 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Order Parameter for HII phase On 2/22/17 9:51 PM, Mohsen Ramezanpour wrote: Dear Gromacs users, Unfortunately, I did not get any reply on this post.

Re: [gmx-users] Order Parameter for HII phase

2017-02-23 Thread Justin Lemkul
...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 23 February 2017 12:16 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Order Parameter for HII phase On 2/22/17 9:51 PM, Mohsen Ramezanpour wrote: Dear Gromacs users

Re: [gmx-users] Order Parameter for HII phase

2017-02-23 Thread Mohsen Ramezanpour
gt; >> Cheers >> >> Tom >> >> ________ >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin >> Lemkul [jalem...@vt.edu] >> Sent: 23

Re: [gmx-users] Order Parameter for HII phase

2017-02-23 Thread Mohsen Ramezanpour
t; molecular frame. > > Cheers > > Tom > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin > Lemkul [jalem...@vt.edu] > Sent: 23 February 2017 12:16 > To

Re: [gmx-users] Order Parameter for HII phase

2017-02-23 Thread Piggot T .
s.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 23 February 2017 12:16 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Order Parameter for HII phase On 2/22/17 9:51 PM, Mohsen Ramezanpour wrote: > Dear Gromacs users, > > Unfortunately, I did not get any

Re: [gmx-users] Order Parameter for HII phase

2017-02-23 Thread Justin Lemkul
On 2/22/17 9:51 PM, Mohsen Ramezanpour wrote: Dear Gromacs users, Unfortunately, I did not get any reply on this post. I was wondering if anyone is aware of the original paper on g_order so that I can understand the underlying algorithm of the options? I am not sure how to use it for HII phas

Re: [gmx-users] Order Parameter for HII phase

2017-02-22 Thread Mohsen Ramezanpour
Dear Gromacs users, Unfortunately, I did not get any reply on this post. I was wondering if anyone is aware of the original paper on g_order so that I can understand the underlying algorithm of the options? I am not sure how to use it for HII phase order parameters. I found this article but I am

[gmx-users] Order Parameter for HII phase

2017-02-16 Thread Mohsen Ramezanpour
Dear Gromacs users, I am interested in calculation of order parameter of lipids in a HII phase. I am not sure about the correct command to use. Which one of the following should I use to be able to compare my data with deutirated NMR experiments? 1) gmx order -f md.xtc -n index.ndx -s md.t