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

[Apramita Chand]

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 pressure had
converged to its desired values within 10ns. Why do we need to give longer
equilbration times?

Please advise.

yours sincerely
Apramita







> Message: 4
> Date: Sun, 4 Jun 2017 13:39:18 -0300
> F
>
> 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 is your case, 10 ns is certainly too short for equilibration and
20
> ns is also way too short for structural sampling, I would increase both by
> maybe 5-10 fold longer if proper relaxation and sampling are expected (how
> long is long enough can be monitored by the time evolution of the
> properties of interest - only when plateaus are obtained you can begin the
> production run)
>
> Andre
>
>
> On Sun, Jun 4, 2017 at 12:39 PM, Apramita Chand <apramita.chand at gmail.com>
> wrote:
>
> > 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 > > -- > > Gromacs Users mailing list*