Re: [gmx-users] protein protein interaction: side chain contribution

2017-07-09 Thread Tushar Ranjan Moharana
Hi Justin, Thanks a lot for the valuable advice. "A society with free knowledge is better than a society with free food" On Fri, Jul 7, 2017 at 3:04 PM, Tushar Ranjan Moharana < tusharranjanmohar...@gmail.com> wrote: > Hi Justin, > Thanks a lot for the advice. It looks like I had put one at

Re: [gmx-users] protein protein interaction: side chain contribution

2017-07-07 Thread Justin Lemkul
On 7/7/17 5:34 AM, Tushar Ranjan Moharana wrote: Hi Justin, Thanks a lot for the advice. It looks like I had put one atom in the wrong index group. After correction my results looks as follows: Energy Average Err.Est. RMSD Tot-Drift ---

Re: [gmx-users] protein protein interaction: side chain contribution

2017-07-07 Thread Tushar Ranjan Moharana
Hi Justin, Thanks a lot for the advice. It looks like I had put one atom in the wrong index group. After correction my results looks as follows: Energy Average Err.Est. RMSD Tot-Drift --- Cou

Re: [gmx-users] protein protein interaction: side chain contribution

2017-07-05 Thread Justin Lemkul
On 7/3/17 4:20 AM, Tushar Ranjan Moharana wrote: Hi all, I want to know the contribution of various amino acid side chain in complex that composed of 2 proteins. I used GROMOS53a6 forcefiel for the simulation. All parameters are as recommended by the concerned paper. I made separate index group

[gmx-users] protein protein interaction: side chain contribution

2017-07-03 Thread Tushar Ranjan Moharana
Hi all, I want to know the contribution of various amino acid side chain in complex that composed of 2 proteins. I used GROMOS53a6 forcefiel for the simulation. All parameters are as recommended by the concerned paper. I made separate index groups for each amino acid side chain and the proteins. I