[gmx-users] g_sham

Naba nabajyoti.goswami at gmail.com
Fri Aug 14 07:14:26 CEST 2015 

Thank you very much Micholas.
I have actually done the second option. But I was uncertain whether I have
done are all nonsense.
>From your replies it seems that I am quite close to fulfill my objectives.
Meanwhile, I am about to perform dPCA for those loops as you have suggested
in the previous mail.
Thanks a lot.

On Thu, Aug 13, 2015 at 5:32 PM, Smith, Micholas D. <smithmd at ornl.gov>
wrote:

> Hi Naba,
>
> I believe you would want to do your second option if you want to include
> the contributions from all of the loops. If you are just interested in one
> loop, then you would do each seperately. Rule-of-thumb for these
> calculations are whatever group you use for the convariance matrix, is what
> you should use for the 2D projection.
>
> Hope that helps.
>
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Naba <
> nabajyoti.goswami at gmail.com>
> Sent: Thursday, August 13, 2015 4:17 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] g_sham
>
> Thanks for the reply Micholas.
>
> I read the special discussion on dPCA at your provided link. But that is a
> fact of small peptide penta-alanine.
> I actually completed a 100 ns simulation of a outermembrane protein (of 239
> amino acid residues) with 284 DMPC molecules. The protein contains 4
> extracellular loops of variable lengths and I want to study the dynamics of
> these loops. What I wanted to confirm is:
>
> 1. Is it all right if I extract covariance separately for each loops? OR,
> 2. Should I calculate covariance of index groups of my concerned loops and
> then should I proceed to 2D projection (by g_anaeig)?
>
>
> On Fri, Aug 7, 2015 at 5:50 PM, Smith, Micholas D. <smithmd at ornl.gov>
> wrote:
>
> > >1. Is it feasible to obtain free energy landscape (FEL) from a 2D
> > >projection (using g_anaeig) of  index groups (say some loop's atoms)
> which
> > >are used for the least squares fit in g_covar and then selecting index
> > >group of elements that corresponds to the eigenvectors (say
> Prot-masses)?
> > >Or,
> > >Should I calculate covariance (g_covar) of my concerned loops separately
> > >and then should I go for g_sham?
> >
> > I am not sure if I understand, however, I think I may be able to help a
> > litttle. g_sham is just a histograming program that inverts the resulting
> > histogram into energy space, so using a 2D projection is a legitimate
> use.
> > Indeed what you are trying to do is very similar to the steps used in
> dPCA
> > (see:
> >
> http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca
> > ).
> >
> > >2. Is there any representative way to get the exact time point for the
> > >corresponding minima obtained from g_sham?
> >
> > If you have the time series for each of the coordinates used in the 2D
> > projection you just need to scan through the 2D timeseries for values
> that
> > match the minimia. e.g. If in the g_sham a minima is at coordinates
> (10,10)
> > than you need to scan through the timeseries of your coordinates:
> > time coord1 coord2
> > 1         0        0
> > 2         1       10
> > 3         40     400
> > 4        10        25
> > .......
> > .......
> > 5000  10     10
> > .....
> > 6000   10    10
> > .....
> > 988908   10  10
> > ....
> >
> >
> > where frames 988908, 5000, and 6000 are the ones you are looking for. You
> > could extract these with
> >
> > awk -v x=coord1min -v y=coord2min 'BEGIN{while(getline <
> >
> "yourfile_first_coordinate_here.xvg"){if($0!~/#/&&$0!~/@/&&$0!~/&/){a[$1]=$2}}{if($0!~/#/&&$0!~/@/&&$0!~/&/){if(a[$1]==x&&$2==$y){print
> > $1}}' yourfile_second_coordinate_here.xvg
> >
> > where you would provide the x and y coords of the minina where I have
> > coord1min and coord2min.
> >
> > You may be more interested in getting frames near the minimia and not
> > actually on it, in which case just change the last if-statement as
> needed.
> >
> > Hope that helps.
> >
> > -Micholas
> >
> > ===================
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> >
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Naba <
> > nabajyoti.goswami at gmail.com>
> > Sent: Friday, August 07, 2015 12:57 AM
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] g_sham
> >
> > Dear All,
> > I searched a lot more things about g_sham in the mailing list and
> > eventually getting confused with the inputs. Just make me clear about:
> >
> > 1. Is it feasible to obtain free energy landscape (FEL) from a 2D
> > projection (using g_anaeig) of  index groups (say some loop's atoms)
> which
> > are used for the least squares fit in g_covar and then selecting index
> > group of elements that corresponds to the eigenvectors (say Prot-masses)?
> > Or,
> > Should I calculate covariance (g_covar) of my concerned loops separately
> > and then should I go for g_sham?
> >
> > 2. Is there any representative way to get the exact time point for the
> > corresponding minima obtained from g_sham?
> >
> >
> > Thanks for all previous helps...
> > Naba
> >
> > Bioinformatics Infrastructure Facility
> > Department of Animal Biotechnology
> > College of Veterinary Science
> > Khanapara,Guwahati 781022
> > Assam, India
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>
> --
> Nabajyoti Goswami
>
> Research Associate
> Bioinformatics Infrastructure Facility
> Department of Animal Biotechnology
> College of Veterinary Science
> Khanapara,Guwahati 781022
> Assam, India
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> Gromacs Users mailing list
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-- 
Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India

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