[gmx-users] g_sham

Tue Aug 25 09:18:32 CEST 2015

It's working now. Thanks a lot.
One more query:
If I am interested in getting frames near the minimia and not actually on
it, how do I change the last if-statement?

On Mon, Aug 24, 2015 at 5:45 PM, Smith, Micholas D. <smithmd at ornl.gov>
wrote:

> My bad, I had a typo, try this one:
>
> awk -v x=firstcoordmin -v y=secondcoordmin 'BEGIN{while(getline
> <"first_coordinate_file_here.xvg"){if($0!~/#/&&$0!~/@/&&$0!~/&/){a[$1]=$2}}}NR>0{if($0!~/#/&&$0!~/@/&&$0!~/&/){if(a[$1]==x&&$2==y){print
> $1}}}' second_coordinate_file_here.xvg
>
> ===================
> 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: Saturday, August 22, 2015 4:16 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] g_sham
>
> Dear Micholas,
>
> The awk command that you have suggested as:
>
> 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
>
> is not working. It says "^ unexpected newline or end of string". I have
> supplied my coord1min, coord2min,  yourfile_first_coordinate_here.xvg and
> yourfile_second_coordinate_here.xvg.
>
> can you please re-write the command with correct syntax please?
>
> On Fri, Aug 14, 2015 at 10:44 AM, Naba <nabajyoti.goswami at gmail.com>
> wrote:
>
> > 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
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
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> >> > posting!
> >> >
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> >> >
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> >> > send a mail to gmx-users-request at gromacs.org.
> >> >
> >> > --
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> >> >
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> >> > posting!
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> >> > send a mail to gmx-users-request at gromacs.org.
> >> >
> >>
> >>
> >>
> >> --
> >> Nabajyoti Goswami
> >>
> >> Research Associate
> >> Bioinformatics Infrastructure Facility
> >> Department of Animal Biotechnology
> >> College of Veterinary Science
> >> Khanapara,Guwahati 781022
> >> Assam, India
> >> --
> >> 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.
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
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> >> posting!
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> >>
> >
> >
> >
> > --
> > Nabajyoti Goswami
> >
> > Research Associate
> > Bioinformatics Infrastructure Facility
> > Department of Animal Biotechnology
> > College of Veterinary Science
> > Khanapara,Guwahati 781022
> > Assam, India
> >
>
>
>
> --
> Nabajyoti Goswami
>
> Research Associate
> Bioinformatics Infrastructure Facility
> Department of Animal Biotechnology
> College of Veterinary Science
> Khanapara,Guwahati 781022
> Assam, India
> --
> 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-request at gromacs.org.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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>

-- 
Nabajyoti Goswami

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