[gmx-users] [EXT] Re: Density of POPC membrane and lateral diffusion
Smith, Iris
smithi4 at ccf.org
Mon Aug 27 15:25:38 CEST 2018
Thank you Kevin - I will extend the simulation time from 20ns in order to obtain enough sampling.
Iris
Iris Nira Smith | Postdoctoral Fellow | Genomic Medicine Institute
Cleveland Clinic | 9500 Euclid Ave. / NE5-255 | Cleveland, OH 44195 | (216) 445-7885
On 8/21/18, 10:55 AM, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Kevin Boyd" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of kevin.boyd at uconn.edu> wrote:
Hi,
In general, I'd say that 20 ns is far too short for a membrane simulation,
but how long of a simulation is needed depends on what you're trying to
calculate - lipid tail dynamics are quite fast, but head group dynamics are
significantly slower. For some membrane-protein interactions, slow dynamics
can lead to some really ridiculous simulation times needed to get proper
statistics, see e.g.
Neale C, Hsu JCY, Yip CM, Pomès R. Indolicidin Binding Induces Thinning of
a Lipid Bilayer. *Biophysical Journal*. 2014;106(8)
Other things like equilibrium between lipid head groups and ions in
solution can take 10s to 100s of nanoseconds.
1. Lipids wouldn't jump across a water barrier. What are you using to check
the density of the system? You should be using options that center on the
membrane, and gmx density should account for periodic boundary conditions.
2. MSD curves are only linear past a certain time lag, so you need to fit
the linear portion of the curve (use beginfit and endfit for gmx msd) - see
some msd plots for examples of what the curve should look like. I very much
doubt you have enough sampling to get a well-resolved linear region for the
lipids with 20 ns of data, but how quickly that curve is resolved will
depend on how many lipids you have. You absolutely don't have enough
sampling to calculate the diffusion of the protein. Since you only have 1
data point (as opposed to a bunch of lipids), and protein diffusion is much
slower, you'd probably need sampling on the order of hundreds of
nanoseconds to microseconds for that.
Kevin
On Tue, Aug 21, 2018 at 7:49 AM, Smith, Iris <smithi4 at ccf.org> wrote:
> Good Morning GROMACS users,
>
> I recently ran a 20 ns production run for my protein-membrane system
> (POPC).
>
> I calculated the density of the membrane and lateral diffusion of lipids
> for my system and I have a couple of questions. I ran a short production
> run to test if my system was stable enough, so I’m not sure if it’s long
> enough to measure these two key parameters.
>
>
> 1. For the density of the membrane, it appears that my water is not
> distributed evenly and that I may have PBC issues due to asymmetry (lipids
> jumping). I added a layer of water at the bottom of my box – could it be
> that I did not add enough water which is causing my lipids to jump?
>
>
> 1. For lateral diffusion, I’m not sure if the value (see below) is
> representative of the diffusion coefficient of POPC in water given the
> short simulation – should the system be run longer in order to achieve an
> appropriate value?
>
> $ gmx msd -s md_20.tpr -f md_20.xtc -n p.ndx -lateral z
>
> ...
>
> Selected 22: 'P'
> Last frame 10000 time 20000.000
>
> Used 2001 restart points spaced 10 ps over 20000 ps
>
> Fitting from 2000 to 18000 ps
>
> D[ P] 0.007966 (+/- 0.001864) 1e-5 cm^2/s
>
> Thank you, Iris
>
>
>
> [/Users/smithi4/Library/Containers/com.microsoft.
> Outlook/Data/Library/Caches/Signatures/signature_1451095126]
>
> Iris Nira Smith | Postdoctoral Fellow | Genomic Medicine Institute
> Cleveland Clinic | 9500 Euclid Ave. / NE5-255 | Cleveland, OH 44195 |
> (216) 445-7885
>
>
>
>
> ===================================
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the country
> by U.S. News & World Report (2017-2018). Visit us online at
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.
> clevelandclinic.org&data=02%7C01%7Ckevin.boyd%40uconn.edu%
> 7C299daceec8604adc706808d6075c44c1%7C17f1a87e2a254eaab9df9d439034
> b080%7C0%7C0%7C636704490223139831&sdata=1gcTvwp7hnj240wuM%
> 2BibKm0fGcsiKlFrvMmOoRuXuuI%3D&reserved=0 for a complete listing of
> our services, staff and locations. Confidentiality Note: This message is
> intended for use only by the individual or entity to which it is addressed
> and may contain information that is privileged, confidential, and exempt
> from disclosure under applicable law. If the reader of this message is not
> the intended recipient or the employee or agent responsible for delivering
> the message to the intended recipient, you are hereby notified that any
> dissemination, distribution or copying of this communication is strictly
> prohibited. If you have received this communication in error, please
> contact the sender immediately and destroy the material in its entirety,
> whether electronic or hard copy. Thank you.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at https://na01.safelinks.
> protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%
> 2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%
> 7C01%7Ckevin.boyd%40uconn.edu%7C299daceec8604adc706808d6075c44c1%
> 7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636704490223149835&sdata=
> MqTfdKhTX1R51JwhXfASDtmHjgzeW12QxVlwWHcJuSI%3D&reserved=0 before
> posting!
>
> * Can't post? Read https://na01.safelinks.protection.outlook.com/?url=
> http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&
> data=02%7C01%7Ckevin.boyd%40uconn.edu%7C299daceec8604adc706808d6075c44c1%
> 7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636704490223149835&sdata=
> 8WBOWtrw1KlVwzwdwX9RzA3NpApJ1vB2qCumjDS%2B6Z8%3D&reserved=0
>
> * For (un)subscribe requests visit
> https://na01.safelinks.protection.outlook.com/?url=
> https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%
> 2Fgromacs.org_gmx-users&data=02%7C01%7Ckevin.boyd%40uconn.edu%
> 7C299daceec8604adc706808d6075c44c1%7C17f1a87e2a254eaab9df9d439034
> b080%7C0%7C0%7C636704490223149835&sdata=GcG4PTYDN3kVP29JXpE0AeIucQQT5v
> CG87nd1Nkd%2FX4%3D&reserved=0 or send a mail to
> gmx-users-request at 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-request at gromacs.org.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
More information about the gromacs.org_gmx-users
mailing list