[gmx-users] Re: dPCA

[Gia Maisuradze]

Dear David,

Thanks for your reply. I have seen -or option in Gromacs 3.3 RC2 version and 
made a trajectory file from g_angle. Then I have generated new topology file 
(tpr) for dihedral angles by using tpbconv. After that I used trr (obtained 
from g_angle) and tpr (obtained from tpbconv) and angle.ndx (obtained from 
mk_angndx) in g_covar to get eigenvactors and eigenvalues, and I got 
Segmentation fault. When I was creating all these files I was asked which 
group of dihedrals I want to include, I have picked one of them for all 
files (I don't know the comand which can include all groups).

I don't know why I got segmentation fault, any idea? Could it be related to 
index file?

Thanks in advance,

Gia

----- Original Message ----- 
From: "David van der Spoel" <spoel at xray.bmc.uu.se>
To: <gmx-users at gromacs.org>
Sent: Monday, October 17, 2005 10:29 PM
Subject: [gmx-users] Re: dPCA


> On Mon, 2005-10-17 at 17:51 -0700, Gia Maisuradze wrote:
>> 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?
> Use the -h option then you will see that you need -or
> The index file you may need to make yourself.
>
> Please put further questions on the mailing list.
>>
>> 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
>> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> >
>> >
>
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