Re: [gmx-users] NVT equilibration of protein on membrane surface

he protein is on the membrane surface). Thank you so much for your help. Olga ‫בתאריך יום ב׳, 28 באוק׳ 2019 ב-14:59 מאת ‪Justin Lemkul‬‏ <‪jalem...@vt.edu ‬‏>:‬ > > > On 10/28/19 3:27 AM, Olga Press wrote: > > Prof. Justin thanks so much for the explanation. > > Why this pheno

Re: [gmx-users] NVT equilibration of protein on membrane surface

) will be sufficient to fix the problem? Thanks a lot Olga ‫בתאריך יום א׳, 27 באוק׳ 2019 ב-20:45 מאת ‪Justin Lemkul‬‏ <‪jalem...@vt.edu ‬‏>:‬ > > > On 10/27/19 1:20 PM, Olga Press wrote: > > Prof. Justin thank you for replay. > > The leaflets are not simply separatin

Re: [gmx-users] NVT equilibration of protein on membrane surface

ards, Olga ‫בתאריך יום א׳, 27 באוק׳ 2019 ב-18:04 מאת ‪Justin Lemkul‬‏ <‪jalem...@vt.edu ‬‏>:‬ > > > On 10/27/19 11:10 AM, Olga Press wrote: > > Dear Gromacs users, > > I run 10ns NVT equilibration with position restains (on the protein) for > a > > system in which the

[gmx-users] NVT equilibration of protein on membrane surface

is attached to the mail. I think that it is the issue of the center-of-mass motion removal, but I'm not sure and would be very grateful for any suggestions. Best regards, Olga -- *Olga Press-Sandler* Ph.D. student, Yifat Miller's lab Department of Chemistry Ben-Gurion University, Israel -- Gromacs Users

[gmx-users] Temperature coupling group and center-of-mass (COM) motion removal in simulation of protein on membrane surface

of embedded proteins? 2. Should the bilayer COM and solvent COM must be reset separately in the following way: comm-grps = Protein_DOPC SOL_CLA_SOD? Thanks in advance. Olga *Olga Press-Sandler* Ph.D. student, Yifat Miller's lab Department of Chemistry Ben-Gurion University, Israel -- Gromacs

Re: [gmx-users] Solvation of protein on membrane surface

Thanks a lot for your help. ‫בתאריך יום ב׳, 21 באוק׳ 2019 ב-19:51 מאת ‪Justin Lemkul‬‏ <‪jalem...@vt.edu ‬‏>:‬ > > > On 10/20/19 5:57 AM, Olga Press wrote: > > Prof. Lemkul, > > Thank you very much for your reply. I would be very grateful if you can > > help

Re: [gmx-users] Solvation of protein on membrane surface

lot! Olga ‫בתאריך יום ב׳, 7 באוק׳ 2019 ב-18:23 מאת ‪Justin Lemkul‬‏ <‪jalem...@vt.edu ‬‏>:‬ > > > On 10/7/19 3:30 AM, Olga Press wrote: > > Dear all, > > I would like to perform a simulation of protein on a membrane surface. > > Following the placement of the protein on

[gmx-users] Solvation of protein on membrane surface

lem? Thank you. -- *Olga Press-Sandler* Ph.D. student, Yifat Miller's lab Department of Chemistry Ben-Gurion University, Israel -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

Re: [gmx-users] Simulation of membrane associated protein

Thank you! *Olga Press-Sandler* Ph.D. student, Yifat Miller's lab Department of Chemistry Ben-Gurion University, Israel -- 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

[gmx-users] Solvation of protein on membrane surface .JPG

I've shared an item with you: Solvation of protein on membrane surface .JPG https://drive.google.com/file/d/1cdYTCn7PLrRrt4aUSHz40WTLG7QZ9xzP/view?usp=sharing=5d9ae82d It's not an attachment -- it's stored online. To open this item, just click the link above. Dear all, I would like to

Re: [gmx-users] Simulation of membrane associated protein

g! > > * 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. > -- *Olga Press-Sandler* Ph.D. student, Yifat Mi

[gmx-users] Simulation of membrane associated protein

y help. Thank you! -- *Olga Press-Sandler* Ph.D. student, Yifat Miller's lab Department of Chemistry Ben-Gurion University, Israel -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Rea

[gmx-users] analysis following the equlibration of protein-membrane system

Dear Gromacs users, I've performed a membrane-protein simulation by charmm36ff as described below: 1. 10ns of NVT equilibration with position restrained on the protein 2. 50ns of NPT equilibration with position restrained on the protein 3. 200ns of NPT equilibration without position restrained

Re: [gmx-users] npt equlibration without position restrain

Thank you very much for your help. Olga ‫בתאריך יום א׳, 20 בינו׳ 2019 ב-22:35 מאת ‪Mark Abraham‬‏ <‪ mark.j.abra...@gmail.com‬‏>:‬ > Hi, > > They're inactive so whether they have any value or are present does not > matter. > > Mark > > On Sun., 20 Jan. 2019, 10:34

Re: [gmx-users] npt equlibration without position restrain

bra...@gmail.com‬‏>:‬ > Hi, > > If you're not using position restraints then options that affect how they > work are inactive. > > Mark > > On Sun., 20 Jan. 2019, 09:46 Olga Press, wrote: > > > Dear gromacs users, > > > > I perform membrane-protein simu

[gmx-users] npt equlibration without position restrain

Dear gromacs users, I perform membrane-protein simulation and used the same mdp files as suggested by the tutorial of Dr. Justin Lemkul with one exception of changing the correct parameters for charmm36ff as suggested by gromacs manual. I performed 10ns of *NVT equilibration with position

Re: [gmx-users] membrane pre-equilibration

t the > protein, unless you have a good reason not to. > > Kevin. > > On Sun, Oct 7, 2018 at 7:23 AM Olga Press wrote: > > > Dear all, > > I'm new in the field of simulating membrane-protein system in gromacs by > > using charmm36-ff. > > I've used c

[gmx-users] membrane pre-equilibration

Dear all, I'm new in the field of simulating membrane-protein system in gromacs by using charmm36-ff. I've used charmm-gui membrane builder to contract pure DOPC bilayer and followed the "README" file. Which analysis should I perform* before* embedding the protein into the membrane to ensure

Re: [gmx-users] membrane-protein system by using charmm36 ff

>> The choices for thermostats/barostats for all equilibration and >> production runs should be appropriate. >> >> Alex >> >> >> On 6/18/2018 2:50 AM, Olga Press wrote: >> >>> Thank you for your help! >>> How important is it to make a good

Re: [gmx-users] membrane-protein system by using charmm36 ff

timescale. It is in fact quite short. > > > > On Sun, Jun 17, 2018 at 1:25 PM Olga Press wrote: > > > Dear Gromacs users, > > I'm new in the field of Molecular Dynamics especially in using Gromacs. > > I have several questions regarding mdp file and I'll be very gr

[gmx-users] membrane-protein system by using charmm36 ff

Dear Gromacs users, I'm new in the field of Molecular Dynamics especially in using Gromacs. I have several questions regarding mdp file and I'll be very grateful if you can help me with them. I'm using a membrane-protein system with Charmm36 ff. After I have constructed bilayer membrane by using