Hi Everyone, Like to know your thoughts on this. I appreciate any comment on this in advance.
Cheers, Mohsen On Wed, Oct 18, 2017 at 7:26 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Justin, Tom, Antonio, > > I read the articles recommended in the previous emails. > To get the order parameter, for any system and by any technique (e.g. > g_angle), we need to calculate the C-D vector angle with respect to the > "local normal vector" at the place of that lipid. > > For the bilayer, it is the Z direction which is the normal vector to the > bilayer surface. Easy. > > For the HII, however, this "local normal vector" is challenging. > The cylinders in HII (which is long enough) are not perfect cylinders and > are bent (in a shape like a Tilda "~" ). Even when the cylinders are not > bent (i.e.they are like "__", still a "local normal vector" need to be > calculated in this calculation. > > > Here are four solutions I am thinking about: > > 1) Using the "radial" option in g_order, but I am not sure if this will > give what I want. > > 2) Slicing the HII cylinders in Z direction (i.e. the cylinder axis), > calculating a center of mass for those lipids in each slice, and then using > the g_angle and its "-g2 sphnorm". In this way, the COM of that slice will > be taken as the center of the sphere (an approximation). > > 3) Using g_angle but using "-g1 plane": in this case, the coordinates of > three atoms in that lipid at each frame will be used to make the local > normal vector. > > 4) Maybe a combination of g_sgangle and g_angle/g_order. The > g_sgangle seems to give the local normal vector for each time frame. This > can be subsequently used in g_order or g_angle for angle calculation. > > One of the main problems in methods 3 and 4 is that: the way the three > atoms on the lipid are selected, the normal vector will be different, > especially if the lipid is tilted. > > Is there any other way which I could calculate the C-D angle and order > parameter in HII phase? > > Please let me know your opinion. Any help is appreciated in advance. > > Cheers, > Mohsen > > On Thu, Feb 23, 2017 at 4:55 PM, Mohsen Ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > >> Thanks Antonio. >> I will give them a try :-) >> >> Cheers >> Mohsen >> >> On Thu, Feb 23, 2017 at 4:15 PM, Antonio Baptista <bapti...@itqb.unl.pt> >> wrote: >> >>> Hi Mohsen, >>> >>> I suggest you have a look at the QRB 1977 review by Seelig, that Tom >>> already mentioned. Like for the planar case, they discuss how spectra of >>> cylindrical lipid phases are related to the order parameter tensor (but I >>> never looked into the details for that case). Anyway, I don't know if you >>> want to compare your simulations with experimental data or are just looking >>> for a convenient structural parameter. But, whatever the case is, reading >>> the literature and thinking about the geometry of your system (Duliez's >>> papers are a good train for that) should give you some hints for a relevant >>> parameter for your system. >>> >>> Once you have selected a parameter, you can compute it from stratch >>> using other GROMACS tools besides g_order. In particular, you can use >>> g_gangle to get several sorts of angles and then process them yourself. As >>> an example, you can use this approach to compute SCD using the equation >>> already mentioned by Tom, and then check if it agrees with the SCD given by >>> g_order (I once did that, just to be sure). >>> >>> Good luck! :) >>> >>> Best, >>> Antonio >>> >>> >>> >>> On Thu, 23 Feb 2017, Justin Lemkul wrote: >>> >>> >>>> >>>> On 2/23/17 1:25 PM, Mohsen Ramezanpour wrote: >>>> >>>>> And I agree with Piggot. The paper by Chau is about on option in >>>>> g_order. >>>>> >>>>> >>>> Yes, and if memory serves (been a while since I used the program, so >>>> perhaps I am confusing something), this is what -o provides you so I >>>> thought it was relevant. -od gives you the deuterium order parameters. >>>> The documentation for gmx order is indeed very sparse. >>>> >>>> Anyway, a general question: >>>>> Can we expect to find a published article for each/some module(s) in >>>>> Gromacs? >>>>> >>>> >>>> No. Many of the tools are just implementations of simple algorithms >>>> used widely in simulations. Some do have specific references and those are >>>> generally printed to the screen output in bold blocks of text. >>>> >>>> With regards to deuterium order parameters, there is a well accepted >>>> and ubiquitously used equation, which Tom posted. >>>> >>>> I mean how/where can we figure out the underlying algorithm and >>>>> comprehensive description of each analysis tool? >>>>> >>>>> >>>> That's why GROMACS is open source :) Efforts are certainly always made >>>> to provide references when possible. >>>> >>>> -Justin >>>> >>>> Cheers >>>>> Mohsen >>>>> >>>>> >>>>> On Thu, Feb 23, 2017 at 10:06 AM, Mohsen Ramezanpour < >>>>> ramezanpour.moh...@gmail.com> wrote: >>>>> >>>>> Hi Justin, Piggot, >>>>>> >>>>>> Thanks for your replies. >>>>>> I agree with that. The problem is that the situation is >>>>>> straightforward >>>>>> for bilayers as bilayers are usually in specific angles regarding the >>>>>> magnetic field (e.g. they are perpendicular, as it is the case in >>>>>> Vermeer study.) >>>>>> For example the normal to the bilayer is z and we do not need be worry >>>>>> about anything else. >>>>>> However, in the case of HII phase, there are cylinders which are not >>>>>> perfectly cylinder. >>>>>> Even if they are perfect cylinders, I think I should use "membrane >>>>>> radial >>>>>> axis" to mimic the local normal vector to the lipid surface. >>>>>> >>>>>> Cheers >>>>>> Mohsen >>>>>> >>>>>> >>>>>> On Thu, Feb 23, 2017 at 8:08 AM, Piggot T. <t.pig...@soton.ac.uk> >>>>>> wrote: >>>>>> >>>>>> Hi, >>>>>>> >>>>>>> I don't believe this Chau paper is for deuterium order parameters >>>>>>> (as I >>>>>>> think you are most likely referring to) but is related to some of >>>>>>> the other >>>>>>> order parameter options in gmx order. The Vermeer paper you mention >>>>>>> gives a >>>>>>> good overview of deuterium order parameters 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 united-atom systems (as gmx order assumes), I believe the >>>>>>> calculation >>>>>>> is 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 appropriate definition of the molecular frame of the >>>>>>> system, >>>>>>> where the z-axis is the bilayer normal. >>>>>>> >>>>>>> Note that if you are calculating order parameters for unsaturated >>>>>>> carbons >>>>>>> (e.g. as in carbon-carbon double bonds), gmx order doesn't currently >>>>>>> do >>>>>>> this correctly as it requires a different calculation with a >>>>>>> different >>>>>>> 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: 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. >>>>>>>> >>>>>>>> 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 not sure if these are the ones, as >>>>>>>> they do >>>>>>>> not describe g_order. >>>>>>>> >>>>>>>> "A new order parameter for tetrahedral configurations" by Chau and >>>>>>>> >>>>>>> Hardwick >>>>>>> >>>>>>>> (1998) >>>>>>>> >>>>>>> >>>>>>> This is the reference given at the end of the gmx order help >>>>>>> description. >>>>>>> >>>>>>> -Justin >>>>>>> >>>>>>> and >>>>>>>> "Acyl chain order parameter profiles in phospholipid bilayers: >>>>>>>> >>>>>>> computation >>>>>>> >>>>>>>> from molecular dynamics simulations and comparison with 2 H NMR >>>>>>>> >>>>>>> experiments" >>>>>>> >>>>>>>> by Vermeer et al. >>>>>>>> >>>>>>>> Thanks in advance for your comments >>>>>>>> Mohsen >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Sun, Feb 19, 2017 at 10:18 AM, Mohsen Ramezanpour < >>>>>>>> ramezanpour.moh...@gmail.com> wrote: >>>>>>>> >>>>>>>> Hi Everyone, >>>>>>>>> >>>>>>>>> I was wondering if someone has any suggestion on the following >>>>>>>>> post, >>>>>>>>> please? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Mohsen >>>>>>>>> >>>>>>>>> ---------- Forwarded message ---------- >>>>>>>>> From: Mohsen Ramezanpour <ramezanpour.moh...@gmail.com> >>>>>>>>> Date: Thu, Feb 16, 2017 at 3:13 PM >>>>>>>>> Subject: Order Parameter for HII phase >>>>>>>>> To: Discussion list for GROMACS users <gmx-us...@gromacs.org> >>>>>>>>> >>>>>>>>> >>>>>>>>> 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.tpr -o >>>>>>>>> order.xvg -od >>>>>>>>> deuter.xvg -d z -szonly >>>>>>>>> >>>>>>>>> or >>>>>>>>> >>>>>>>>> 2) gmx order -f md.xtc -n index.ndx -s md.tpr -o >>>>>>>>> order.xvg -od >>>>>>>>> deuter.xvg -d z >>>>>>>>> (In this case, there are four columns of data (x, y, z for each >>>>>>>>> carbon >>>>>>>>> atom). >>>>>>>>> The column 3 seems to be the same with when we include -szonly) >>>>>>>>> >>>>>>>>> or anything else? >>>>>>>>> >>>>>>>>> Corresponding available experimental data, I assume the second >>>>>>>>> command >>>>>>>>> should be correct in my case . However, I am not sure x or y or >>>>>>>>> what >>>>>>>>> >>>>>>>> to use >>>>>>> >>>>>>>> for judging. >>>>>>>>> >>>>>>>>> Cylinders in HII phase are parallel to the Z axis in my system. >>>>>>>>> >>>>>>>>> Many thanks in advance for your comments >>>>>>>>> Mohsen >>>>>>>>> -- >>>>>>>>> *Rewards work better than punishment ...* >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> *Rewards work better than punishment ...* >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> -- >>>>>>> ================================================== >>>>>>> >>>>>>> Justin A. Lemkul, Ph.D. >>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>>>>> >>>>>>> Department of Pharmaceutical Sciences >>>>>>> School of Pharmacy >>>>>>> Health Sciences Facility II, Room 629 >>>>>>> University of Maryland, Baltimore >>>>>>> 20 Penn St. >>>>>>> Baltimore, MD 21201 >>>>>>> >>>>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>>>> http://mackerell.umaryland.edu/~jalemkul >>>>>>> >>>>>>> ================================================== >>>>>>> -- >>>>>>> Gromacs Users mailing list >>>>>>> >>>>>>> * Please search the archive at http://www.gromacs.org/Support >>>>>>> /Mailing_Lists/GMX-Users_List before posting! >>>>>>> >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>>> * For (un)subscribe requests visit >>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>>> or >>>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>>>> -- >>>>>>> Gromacs Users mailing list >>>>>>> >>>>>>> * Please search the archive at http://www.gromacs.org/Support >>>>>>> /Mailing_Lists/GMX-Users_List before posting! >>>>>>> >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>>> * For (un)subscribe requests visit >>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>>> or >>>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> *Rewards work better than punishment ...* >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> -- >>>> ================================================== >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>> >>>> Department of Pharmaceutical Sciences >>>> School of Pharmacy >>>> Health Sciences Facility II, Room 629 >>>> University of Maryland, Baltimore >>>> 20 Penn St. >>>> Baltimore, MD 21201 >>>> >>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>> http://mackerell.umaryland.edu/~jalemkul >>>> >>>> ================================================== >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at http://www.gromacs.org/Support >>>> /Mailing_Lists/GMX-Users_List before posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>>> >>>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >> >> >> >> -- >> *Rewards work better than punishment ...* >> > > > > -- > *Rewards work better than punishment ...* > -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.