[gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 27

Apramita Chand apramita.chand at gmail.com
Mon Jun 5 11:02:05 CEST 2017


On Jun 5, 2017 4:50 AM, <gromacs.org_gmx-users-request at maillist.sys.kth.se>
wrote:
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> Today's Topics:
>
>    1. RMSD Matrix error (Apramita Chand)
>    2. Re: EM error (?Mohammad Roostaie? ?)
>    3. Difference in properties when method of adding urea molecules
>       is changed in a simulation box (Apramita Chand)
>    4. Re: Difference in properties when method of adding urea
>       molecules is changed in a simulation box (Andr? Farias de Moura)
>    5. Re: Difference in properties when method of adding urea
>       molecules is changed in a simulation box (Mark Abraham)
>    6. Negative deuterium order parameters (Poncho Arvayo Zatarain)
>
>
> ----------------------------------------------------------------------
>
> Mess
>
> 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
> >
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>
>
>
> --
> _____________
>
> Prof. Dr. Andr? Farias de Moura
> Department of Chemistry
> Federal University of S?o Carlos
> S?o Carlos - Brazil
> phone: +55-16-3351-8090
>
>
> ------------------------------
>
> Message: 5
> Date: Sun, 04 Jun 2017 17:10:29 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Difference in properties when method of
>         adding urea molecules is changed in a simulation box
> Message-ID:
>         <
CAMNuMAQN3RGgktA2jDsJUgXLtaP_jMA6w2N8PWGiLy4D-hWfeA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> 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 Andr? 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
> > > --
> > > 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
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> >
> > --
> > _____________
> >
> > Prof. Dr. Andr? Farias de Moura
> > Department of Chemistry
> > Federal University of S?o Carlos
> > S?o Carlos - Brazil
> > phone: +55-16-3351-8090
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 6
> Date: Sun, 4 Jun 2017 23:18:57 +0000
> From: Poncho Arvayo Zatarain <poncho_8629 at hotmail.com>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Negative deuterium order parameters
> Message-ID:
>         <
CY4PR06MB2408F16F740E394B5257172380F50 at CY4PR06MB2408.namprd06.prod.outlook.com
>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> Hello: I made 5 simulation: pure DPPC+a molecule inside, pure
DPPE+molecule inside, 50% DPPC-50% DPPE+molecule inside, 75%
DPPC-25%DPPE+molecule inside and 25%DPPC-75% DPPE+molecule inside. All the
graphics were fine, but when i plot my system with 25%DPPC-755DPPE+Molecule
inside the graphic of deuterium order parameters is not in order, is very
disordered, with negative and positive values. Is it possible the molecule
modifies the deuterium order parameters when i increase the DPPE %? Does
anybody knows a reference i can read about this? Thanks.
>
>
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> End of gromacs.org_gmx-users Digest, Vol 158, Issue 27
> ******************************************************


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