Re: [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box(Andr?Farias de Moura)

On 6/6/17 2:34 AM, Apramita Chand wrote: Dear Andre, I added around 56 molecules of urea to 966 water. The peptide is just 6 residues and I just wanted to see its preferred conformations as well as hydrogen bonding. I will definitely try to extend the simulation to atleast 100ns. For the equili

Re: [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box(Andr?Farias de Moura)

Dear Andre, I added around 56 molecules of urea to 966 water. The peptide is just 6 residues and I just wanted to see its preferred conformations as well as hydrogen bonding. I will definitely try to extend the simulation to atleast 100ns. For the equilibration, I found that the temperature and pre

Re: [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box

Hi, Further, I would measure the distribution of the lifetime of hydrogen bonds, since you need to sample much longer than eg the average. And you should also try to measure the autocorrelation time of the number of hydrogen bonds - you don't have a "new" observation until you've simulated at leas

Re: [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box

Hi Apramita, you have not told us how many urea molecules you have added to you system, neither have you told how large your peptide of interest is, but usually people studying denaturation of peptides use very concentrated urea solutions (typically 8 M or so), which are highly viscous. If this i

[gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box

Dear All, I have tested with two ways of solvating a peptide with urea-water mixture Method 1: Pre-equilibrating a urea-water box and solvating the peptide with -cs option with this box Method 2: Adding urea molecules to peptide box using -ci option and then solvating the resulting box with water