Re: [gmx-users] PROTEIN FOLDING

On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta wrote: > Hi gromacs users, > > After MD simulation of protein-ligand complex for 5ns, can we view protein > folding? > > How to do it? > > I want to ascertain if there is any conformation change in protein where > the ligand

Re: [gmx-users] PROTEIN FOLDING

On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta wrote: > Hi gromacs users, > > After MD simulation of protein-ligand complex for 5ns, can we view protein > folding? You can use various supporting tools from R language to debug your trajectory but most third party software

[gmx-users] GROMACS 2018 third beta release

Hi GROMACS users, The third and final beta release of GROMACS 2018 is available! (We know it's only 2017 right now, but by the time we make the real release it will be almost 2018, so that seems like a good idea!) We'll issue a release candidate shortly, and the final release very early in the

Re: [gmx-users] PROTEIN FOLDING

After MD simulation of protein-ligand complex for 5ns, can we view protein folding? mostly, NO Search what time range 'protein folding' is happening. How to do it? I want to ascertain if there is any conformation change in protein where the ligand binds. Is it possible? You might want to do

[gmx-users] PROTEIN FOLDING

Hi gromacs users, After MD simulation of protein-ligand complex for 5ns, can we view protein folding? How to do it? I want to ascertain if there is any conformation change in protein where the ligand binds. Is it possible? We observe hydrogen bonds through molecular docking. Hence, I want to

Re: [gmx-users] Measuring distance to the nearest image

Just wondering whether anyone has had any luck with a similar problem? If not, I’ll knock a script together and make it available. I was hoping not to reinvent the wheel if there was already a way. Regards Anthony On 18/12/2017 06:23, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on

[gmx-users] g_mindsit contact analysis

Hi all, I have simulated a duplex RNA in presence of a CNT in aqueous medium. The gromacs version I used was 4.5.6. The two species were kept 2 nm apart to begin with. I wanted to calculate how many RNA atoms were within 4 angstrom distance from the CNT on a per-frame trajectory basis. I used the

[gmx-users] Free energy perturbation - table extension and blowing system

Hi, I want to calculate 'solvation' energy of lutein in bilayer and water by Free Energy Perturbation. When I'm running a normal MD, or some kind of steering dynamics,my system works just fine. After addition of FEP parameters, em runs, but instantly returns series of warnings: WARNING: Listed

Re: [gmx-users] GROMACS 2018 second beta

Dear Mark, Thank you for all of your efforts. I wish you added an option for applying external magnetic field in this version. Thanks Ali On Mon, Dec 11, 2017 at 8:54 PM, Mark Abraham wrote: > Hi GROMACS users, > > The second beta release of GROMACS 2018 is available!

[gmx-users] PME computation for triclinic box

Good morning, I'd like to ask how PME computations for triclinic box are done in Gromacs. I'd like to compute electric field for my triclinic box and I'm not sure that I understand correctly how it's done in Gromacs. Sincerely, Mariia -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] WHAM

What you will do if you don't have a responsible professor? I tried to install GROMACS in my computer vmware>Ubuntu>... but it wasn't successful and I couldn't.Anyway, you're right I shouldn't discuss these problems here. Thanks again -Rose Sent from my iPhone > On Dec 18, 2017, at 11:58, Alex

Re: [gmx-users] WHAM

On 12/18/2017 1:14 AM, João Henriques wrote: First, you don't need "special computers" to run or compile gromacs. It helps to have multiple compute nodes at your disposal, but it isn't a requirement *per se*. Also, you don't need to be root to compile your own gromacs installation. You can

Re: [gmx-users] WHAM

This has nothing to do with your initial question, but I there are a few misconceptions in your last email that you should be aware of. First, you don't need "special computers" to run or compile gromacs. It helps to have multiple compute nodes at your disposal, but it isn't a requirement *per

[gmx-users] Grompp error : Incorrect number of parameters

Dear all For grompp em.mdp I get an error ERROR 1 [file THC.itp, line 89]: Incorrect number of parameters - found 2, expected 4 or 8 for U-B. My itp file as follows [ angles ] 1 2 29 579.178 109.588 *{Line 89}* 1 2 3 532.192 112.817 2 3 31 551.424

Re: [gmx-users] set computer time on REMD simulation

Sorry, it seems that I did not express my problem clearly. I add "-maxh 0.1", it should be terminated until 10 minutes maximumly. However, the MD did not stop after over one hour. At 2017-12-18 15:48:10, "Qinghua Liao" wrote: >Hello, > >If I understand correctly,