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

[Apramita Chand]

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 molecules

In both the methods, same number of urea and water molecules were added .
10ns equilibration followed by 20ns simulation steps were carried out.
On analysing the properties, average number of hydrogen bonds between
peptide-water in method 1 was 16.221 while it changed to 14.340 in Method
2. Similarly, number of H-bonds between peptide-urea changed from 5.687 to
4.031 on switching from Method 1 to Method 2.

On checking radial distribution functions, interaction between
water-peptide sites were somewhat similar for both Methods but significant
changes were found for peptide-urea site-site correlations. Method-1 showed
higher peptide-urea interaction.

What could be the reason for these discrepancies? Are both methods correct?
I want to go on with Method-2 for further simulations because it is
relatively simpler but Method-1 shows higher hydrogen bonding between sites.

Please suggest.

yours sincerely,
Apramita