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.ch...@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* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
