Re: [gmx-users] Membrane protein simulation isotropic vs semiisotropic

On 6/15/19 8:56 AM, paul buscemi wrote: The pressure on a (real-life) membrane is not isotropic, edges are under tension. so using the p-couple “surface-tension” - with water layers is appropriate. Applying surface tension and semiisotropic coupling will result in different ensembles.

Re: [gmx-users] Membrane protein simulation isotropic vs semiisotropic

The pressure on a (real-life) membrane is not isotropic, edges are under tension. so using the p-couple “surface-tension” - with water layers is appropriate. If you use p-couple = isotropic you should end up with a micelle because the hydrophobic effects are significant. p > On Jun 14,

Re: [gmx-users] Membrane protein simulation isotropic vs semiisotropic

Dear Bratin, When I am using a semiisotropic condition the pbc box is deforming/compressing pushing the lipid bilayer apart. I am attaching the screenshots of the system at the beginning(normal.png) of production run as well as at the end of 30ns simulation (elongated.png) for your reference.

Re: [gmx-users] Membrane protein simulation isotropic vs semiisotropic

Hi Why you want to do isotropic? On Fri 14 Jun, 2019, 12:16 PM Prasanth G, Research Scholar, < prasanthgha...@sssihl.edu.in> wrote: > Dear all, > > Can someone please tell me if it is okay to use isotropic pcoupltype for a > membrane protein simulation? Are there any disadvantages? > > Also,

[gmx-users] Membrane protein simulation isotropic vs semiisotropic

Dear all, Can someone please tell me if it is okay to use isotropic pcoupltype for a membrane protein simulation? Are there any disadvantages? Also, why is semiisotropic preferred over isotropic, in membrane protein simulations.. Thank you. -- Regards, Prasanth. -- Gromacs Users mailing list

Re: [gmx-users] Membrane-protein Simulation

Please don't reply to the whole digest. On 5/6/19 6:47 AM, Sankaran SV . wrote: @email on Membrane protein Simulation: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-May/125180.html Dear Najamuddin Memon Thanks for your reply. I am a little confused here. Why is the

Re: [gmx-users] Membrane-protein Simulation

Group13 (SOL) has 40209 elements > > > > Group14 ( NA) has16 elements > > > > is it ok to make index file (protein+phosphoresidues) for analysis of the > > concatenated trajectory. > > > > Please advise me > > > > T

Re: [gmx-users] Membrane-protein Simulation

Yes it is normal to correct .xtc file through -pbc flag On Thu, May 2, 2019, 12:57 PM Sankaran SV . <119013...@sastra.ac.in> wrote: > Dear all, > > We are investigating the hydration dynamics of membrane proteins (AQP > embedded in DPPC membrane). The topology and the mdp files for simulations >

[gmx-users] Membrane-protein Simulation

Dear all, We are investigating the hydration dynamics of membrane proteins (AQP embedded in DPPC membrane). The topology and the mdp files for simulations was obtained from the MemprotMD database (mdp file: http://memprotmd.bioch.ox.ac.uk/). We modified the temperature of simulation to 310 K

Re: [gmx-users] membrane-protein simulation

Thanks Justin Got it, it's working. On Wed, Aug 2, 2017 at 10:02 AM, Justin Lemkul wrote: > > > On 8/2/17 5:01 AM, Amir Zeb wrote: > >> Hello gmx-user >> >> I want to simulate a membrane protein with more than one chains like A, B, >> C etc. I generated the strong_posre.itp

Re: [gmx-users] membrane-protein simulation

On 8/2/17 5:01 AM, Amir Zeb wrote: Hello gmx-user I want to simulate a membrane protein with more than one chains like A, B, C etc. I generated the strong_posre.itp file as Justing has kindly explained in his tutorial, and updated the topol.top file by inserting the same lines. I also

[gmx-users] membrane-protein simulation

Hello gmx-user I want to simulate a membrane protein with more than one chains like A, B, C etc. I generated the strong_posre.itp file as Justing has kindly explained in his tutorial, and updated the topol.top file by inserting the same lines. I also updated the minim.mdp file by inserting

Re: [gmx-users] membrane protein simulation

Thanks for the reply Tsjerk. In fact I am just wonding if the situation exist, i.e., for the 10th trans-membrane helices in the protein, the 8th and or 9th for example is/are a little shorter than the other several helices. Will you please give a comment on how to process this kind of membrane

[gmx-users] membrane protein simulation

Dear All, Suppose a membrane protein contains 10 trans-membrane helix, and as the cell membrane is round, the upper and lower part of the 10 trans- membrane are not horizontal as they are part of the rounded cell, will you please introduce to me how to make the lipid bilayer in curve to

Re: [gmx-users] membrane protein simulation

Hi Brett, So apart from the curvature of the membrane, there maybe the situation that there's just more of the protein in one leaflet than in the other. You'll need to account for that when embedding. Membrane builders typically check for overlaps to take care of this. Cheers, Tsjerk On Sep 13,

Re: [gmx-users] membrane protein simulation

Dear Tsjerk, Thanks for the reply. Will you please introduce to me sevral membrane builders whith results compatible with gromacs, especially on-line available membrane builders? Best regards. Brett At 2015-09-13 17:45:52, "Tsjerk Wassenaar" wrote: >Hi Brett, >

Re: [gmx-users] membrane protein simulation

Hi Brett, Say I'm designing this new type of truck. Because the earth it's riding over is round, do you think I need to adjust the wheel positions on front and back to match the curvature of the earth? Cheers, Tsjerk On Sep 13, 2015 08:52, "Brett" wrote: > > Dear All, >

Re: [gmx-users] membrane protein simulation

Hi Brett, If you mean an online server, then probably the CHARMM-GUI was made for you. If you mean downloadable, then you can try inflategro or insane (coarse-grained). In addition, Gromacs comes with g_membed integrated. Cheers, Tsjerk On Sep 13, 2015 12:00, "Brett"

Re: [gmx-users] membrane protein simulation

Hi Tsjerk, Yes, it would be very helpful. thanks for your help. Best regards, Mostafa On Thu, Apr 23, 2015 at 9:40 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mostafa, We have a complete simulation system of bacteriorhodopsin in the purple membrane, which you can use as basis for

Re: [gmx-users] membrane protein simulation

Hi Mostafa, We have a complete simulation system of bacteriorhodopsin in the purple membrane, which you can use as basis for your simulations if you want. Best, Tsjerk On Apr 22, 2015 10:08 PM, Mostafa Javaheri javaheri.grom...@gmail.com wrote: Dear Justin I am going to simulate a homo

[gmx-users] membrane protein simulation

Dear Justin I am going to simulate a homo trimer trans-membrane protein; Base on the crystallographic structures there is 7 phosphatidyl glycerol phosphate (PGP) per each monomer and also 3 glycolipid molecules (S-TGA-1, or 3-HSO 3 -Galpβ1-6ManpR1-2GlcpR-1-archeol) located inside the trimer on the

Re: [gmx-users] membrane protein simulation

On 4/22/15 4:07 PM, Mostafa Javaheri wrote: Dear Justin I am going to simulate a homo trimer trans-membrane protein; Base on the crystallographic structures there is 7 phosphatidyl glycerol phosphate (PGP) per each monomer and also 3 glycolipid molecules (S-TGA-1, or 3-HSO 3

Re: [gmx-users] membrane protein simulation - errors

On 9/17/14 6:54 PM, Yunlong Liu wrote: Hi, I am trying to use Gromacs 5.0 to run membrane protein simulation. I built my membrane protein system with POPC membrane and TIP3P water in VMD. Then I used gmx pdb2gmx to build gromacs topology files. My force field is charmm22* and it contains

[gmx-users] membrane protein simulation - errors

Hi, I am trying to use Gromacs 5.0 to run membrane protein simulation. I built my membrane protein system with POPC membrane and TIP3P water in VMD. Then I used gmx pdb2gmx to build gromacs topology files. My force field is charmm22* and it contains a lipids.rtp entry. It can successfully

[gmx-users] membrane protein simulation - ligand introduction

Dear Users If membrane protein ligand complex needs to simulated in lipid bilayers then how to introduce ligand and at what step? regards -- B.Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before