[gmx-users] g_sham

Naba nabajyoti.goswami at gmail.com
Sat Aug 22 10:16:06 CEST 2015 

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
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>>
>>
>>
>> --
>> 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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>> Gromacs Users mailing list
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>> * Please search the archive at
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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

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