[gmx-users] g_sham

[Smith, Micholas D.]

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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