[gmx-users] protein getting unfolded in SPC/E water

Hello, I am simulating Lysozyme in pure SPC/E water for 200 ns. I am using OPLS-AA force field for my work. In pure water the protein looses some of its helices. As for example in the final md.gro file the number of alpha helices observed are 2 while in the beginning 4 were observed in

[gmx-users] help

Dear all, I want to calculate the diffusion coefficient of a single coarse-grained polymer adsorbed on a wall with Gromacs 5.0.7, where the wall's type is 9-3 and the density is set as 1. Firstly, I use the "gmx msd" command to calculate the diffusion coefficient. The calculation error

Re: [gmx-users] anisotropic pressure coupling

Hi Mark, Thanks for your reply. I want anisotropic coupling because I want to have box shape deformation during simulation. Like what has been done in above mentioned article. I have read the manual already, but I am still in doubt. I am pretty sure it should be anisotropic to allow these

Re: [gmx-users] protein getting unfolded in SPC/E water

On 9/15/16 11:46 AM, soumadwip ghosh wrote: Hello, I am simulating Lysozyme in pure SPC/E water for 200 ns. I am using OPLS-AA force field for my work. In pure water the protein looses some of its helices. As for example in the final md.gro file the number of alpha helices observed

Re: [gmx-users] GROMACS 5.1.4 released

Thanks Mark, Should I conclude that "Gromacs 2016" is the version to install if I want to install a fresh version of Gromacs with all the current functionalities ? FR. François-Régis Chalaoux Drug Design, EVOTEC Toulouse De :

Re: [gmx-users] GROMACS 5.1.4 released

Hi, Yes... From the first sentence of my link "These release notes document the functionality changes that have taken place in GROMACS since version 5.1" Mark On Thu, 15 Sep 2016 09:06 Chalaoux, Francois-Regis < francois-regis.chala...@evotec.com> wrote: > Thanks Mark, > > Should I conclude

Re: [gmx-users] anisotropic pressure coupling

Hi, If you want isotropic coupling, don't choose anisotropic. Otherwise, please make sure you read the documentation of the respective .mdp options. Mark On Mon, Sep 12, 2016 at 5:54 PM Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Everyone, > > Please let me know your opinion

Re: [gmx-users] GROMACS 5.1.4 released

Thanks a lot Mark for your "YES" and to stress it. FR. -Message d'origine- De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part de Mark Abraham Envoyé : jeudi 15 septembre 2016 11:44 À : gmx-us...@gromacs.org;