[gmx-users] Re: dPCA

[Gia Maisuradze]

David,

I have tried to do dPCA on Gromacs 3.3 RC2. First, I have generated 
angle.ndx by using mk_angndx where in option -type I wrote dihedral, 
ryckaert-bellemans or phi-psi option does not work. So my angle.ndx looks 
like:
[ Phi=180.0_2_7.11 ]
     1     2     4     5
[ Phi=180.0_2_33.5 ]
     2     4     6     8     8    10    12    14    14    16    18    20

[ Phi=180.0_6_1 ]
     4     6     7     9    10    12    14    16    16    18    20    22

[ Phi=0.0_2_2.09 ]
     5     4     6     8
[ Phi=0.0_0_0 ]
     7     6     8     9    19    20    22    23    20    22    25    24
    20    22    25    26
[ Phi=0.0_6_1 ]
     6     8    10    12    12    14    16    18

then I used angle.ndx along with trajectory and tpr files to produce 
trajectory file for dPCA. In g_angle I wrote for -type option dihedral. Also 
it asks the group to choose, each group has a different number of elements. 
Which one to pick? I found that -oc calculates dihedral autocorrelation 
function. My concern is I could not produce cos(phi) sin(phi) cos(psi) 
sin(psi), as we discussed in our one of the previous emails. Also, the 
dihedral autocorrelation function that I got from -oc option is in xvg 
format, for g_covar I need either xtc or trr format.

Are steps described above correct to perform dPCA? Does Gromacs 3.3 RC2 
support dPCA?

Thanks in advance,

Gia

----- Original Message ----- 
From: "David" <spoel at xray.bmc.uu.se>
To: "Gia Maisuradze" <gia at chem.unr.edu>
Cc: <gmx-users at gromacs.org>
Sent: Thursday, October 13, 2005 1:03 PM
Subject: Re: dPCA


> On Thu, 2005-10-13 at 11:48 -0700, Gia Maisuradze wrote:
>> Dear David,
>>
>> I have checked the changes in new Gromacs 3.3. It says that dihedral
>> PCA is supported in g_angle (you are the author). Does it mean that we
>> can do dihedral principal component analysis for proteins? Is it the
>> same type of analysis that has been done by Gerhard Stock' group
>> (PROTEINS, 58, 45, 2005)? If yes, I don't clearly understand how I can
>> do that. Normal PCA (in cartesian coordinates) can be done by using
>> g_covar, where we build the covariance matrix and diagonalize it, and
>> get eigenvectors and eigenvalues. Then analyze them.
>>
>> Could you, please, explain how I can do dPCA on Gromacs, if it is
>> possible.
> Yes, you use g_angle -oc to produce a new trajectory file containing:
> cos(phi) sin(phi) cos(psi) sin(psi) etc.
> This you run through g_covar.
>
> According to some people this information is not really useful for
> protein analysis, as it can show many false minima and it is hard to go
> back to real space. Barriers you see may be trivial due to overlapping
> atoms.
>
>
>>
>> The same question I have asked Erik Lindahl, but he did not know about
>> dPCA in new Gromacs version.
>>
>> Thanks,
>>
>> Gia
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>