[gmx-users] g_sham

[Naba]

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