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

[Mark Abraham]

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 least that long. Those will probably point to the fact that you aren't
comparing the long sampling time limit in either case.

Mark

On Sun, 4 Jun 2017 18:39 André Farias de Moura <moura at ufscar.br> wrote:

> 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
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>
> --
> _____________
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
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