Re: [gmx-users] Interpretation of g_hbond results

2009-02-24 Thread David van der Spoel 

Justin A. Lemkul wrote:



David van der Spoel wrote:

Justin A. Lemkul wrote:


Hi,

I have a quick question about interpreting the output from g_hbond.  
I am using the -ac option to calculate H-bond lifetimes between my 
protein and a series of different, bound ligands.  I read the 
associated paper, but I would like to confirm the interpretation of 
the results before I continue much further.  I obtained the following:


--
Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward 0.003309.475  19.590  0.000294756
Backward0.007136.034  17.471
One-way 0.002471.990  20.678
Integral0.001   1534.894  23.717
Relaxation  0.002606.619  21.325

The "forward" and "backward" rates and times make sense based on 
equations 3 & 4 in the paper, but I could not find an explanation of 
what "one-way" and "relaxation" are.  Is the "integral" value taken 
from equation 2, and thus should be interpreted as the overall H-bond 
lifetime?


Thanks,
Justin

One-way assumes k' (Backward) rate is zero, Relaxation is the time at 
which C(t) = 1/e
Integral is just the integral of C(t), which in case of exponential 
relation should be the same as the relaxation time (not very close as 
you see).




Thanks, that makes sense.  According to the terminology in your paper, 
then, if k is the rate constant for HB breaking ("forward"), then 1/k is 
the lifetime of the hydrogen bond.  So that lifetime would be the time 
(in ps) given in the "Forward" entry?  It seems simple, I just want to 
be sure since there are a couple of old threads in the archive where 
users claimed that "Backward" was the value to use.


Forward is for breaking, so yes, that is the life time recommended by 
Luzar2000.


Two caveats: first, we recently found out that the numbers in my JPCB 
paper can not be reproduced in 4.0 (embarassingly this was found out 
during a tutorial that I was giving). We are looking into this. Second 
we are busy implementing a new algorithm due to Markovitch * Agmon 
(JCP 129 (2008) p. 084505) that has several advantages over the Luzar 
approach.




My simulations were conducted under 4.0.2, should I not use these 
results? Results from 3.3.x should be correct, since it was used in your 
JPCB paper; but my installation of 3.3.3 gives a segmentation fault on 
our cluster, and a bus error on my local machine.  Are there known 
issues with g_hbond-3.3.3?


As said, we are looking into this. With the original trajectories from 
the paper the 4.0 code gives different values. I haven't tried with 3.3 
analysis tools yet. Digging back into my memory, the problem seems to 
have to do with the correlation function rather than the analysis, that 
is, you can do the Luzar analysis in xmgrace. based on the ACF that 
g_hboond spits out. If you do so you find that you get the same results 
as g_hbond prints, ergo the Luzar analysis is implemented OK, but the 
ACF is suspect.




Or should I just hold off and do analysis after a new version comes out 
and these issues are solved or a new algorithm implemented?


This is up to you to decide...



Thanks again,
Justin


Cheers,





--
David.

David van der Spoel, PhD, Professor of Biology
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
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se

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Re: [gmx-users] Interpretation of g_hbond results

2009-02-24 Thread Justin A. Lemkul 



David van der Spoel wrote:

Justin A. Lemkul wrote:


Hi,

I have a quick question about interpreting the output from g_hbond.  I 
am using the -ac option to calculate H-bond lifetimes between my 
protein and a series of different, bound ligands.  I read the 
associated paper, but I would like to confirm the interpretation of 
the results before I continue much further.  I obtained the following:


--
Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward 0.003309.475  19.590  0.000294756
Backward0.007136.034  17.471
One-way 0.002471.990  20.678
Integral0.001   1534.894  23.717
Relaxation  0.002606.619  21.325

The "forward" and "backward" rates and times make sense based on 
equations 3 & 4 in the paper, but I could not find an explanation of 
what "one-way" and "relaxation" are.  Is the "integral" value taken 
from equation 2, and thus should be interpreted as the overall H-bond 
lifetime?


Thanks,
Justin

One-way assumes k' (Backward) rate is zero, Relaxation is the time at 
which C(t) = 1/e
Integral is just the integral of C(t), which in case of exponential 
relation should be the same as the relaxation time (not very close as 
you see).




Thanks, that makes sense.  According to the terminology in your paper, then, if 
k is the rate constant for HB breaking ("forward"), then 1/k is the lifetime of 
the hydrogen bond.  So that lifetime would be the time (in ps) given in the 
"Forward" entry?  It seems simple, I just want to be sure since there are a 
couple of old threads in the archive where users claimed that "Backward" was the 
value to use.


Two caveats: first, we recently found out that the numbers in my JPCB 
paper can not be reproduced in 4.0 (embarassingly this was found out 
during a tutorial that I was giving). We are looking into this. Second 
we are busy implementing a new algorithm due to Markovitch * Agmon (JCP 
129 (2008) p. 084505) that has several advantages over the Luzar approach.




My simulations were conducted under 4.0.2, should I not use these results? 
Results from 3.3.x should be correct, since it was used in your JPCB paper; but 
my installation of 3.3.3 gives a segmentation fault on our cluster, and a bus 
error on my local machine.  Are there known issues with g_hbond-3.3.3?


Or should I just hold off and do analysis after a new version comes out and 
these issues are solved or a new algorithm implemented?


Thanks again,
Justin


Cheers,


--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Interpretation of g_hbond results

2009-02-24 Thread Justin A. Lemkul 



Manik Mayur wrote:



On Tue, Feb 24, 2009 at 9:44 PM, Justin A. Lemkul > wrote:



Hi,

I have a quick question about interpreting the output from g_hbond.
 I am using the -ac option to calculate H-bond lifetimes between my
protein and a series of different, bound ligands.  I read the
associated paper, but I would like to confirm the interpretation of
the results before I continue much further.  I obtained the following:


Which paper are you talking about? Is there a paper for each gromacs 
postprocessing tool?


Look for this type of information in the output (either to screen or to logs in 
the case of mdrun):


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
J. Phys. Chem. B 110 (2006) pp. 4393-4398
  --- Thank You ---  

I don't know if there is a paper for every single tool, but pertinent algorithms 
are cited when necessary.


-Justin



--
Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward 0.003309.475  19.590  0.000294756
Backward0.007136.034  17.471
One-way 0.002471.990  20.678
Integral0.001   1534.894  23.717
Relaxation  0.002606.619  21.325

The "forward" and "backward" rates and times make sense based on
equations 3 & 4 in the paper, but I could not find an explanation of
what "one-way" and "relaxation" are.  Is the "integral" value taken
from equation 2, and thus should be interpreted as the overall
H-bond lifetime?

Thanks,
Justin

-- 



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur




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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Interpretation of g_hbond results

2009-02-24 Thread David van der Spoel 

Justin A. Lemkul wrote:


Hi,

I have a quick question about interpreting the output from g_hbond.  I 
am using the -ac option to calculate H-bond lifetimes between my protein 
and a series of different, bound ligands.  I read the associated paper, 
but I would like to confirm the interpretation of the results before I 
continue much further.  I obtained the following:


--
Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward 0.003309.475  19.590  0.000294756
Backward0.007136.034  17.471
One-way 0.002471.990  20.678
Integral0.001   1534.894  23.717
Relaxation  0.002606.619  21.325

The "forward" and "backward" rates and times make sense based on 
equations 3 & 4 in the paper, but I could not find an explanation of 
what "one-way" and "relaxation" are.  Is the "integral" value taken from 
equation 2, and thus should be interpreted as the overall H-bond lifetime?


Thanks,
Justin

One-way assumes k' (Backward) rate is zero, Relaxation is the time at 
which C(t) = 1/e
Integral is just the integral of C(t), which in case of exponential 
relation should be the same as the relaxation time (not very close as 
you see).


Two caveats: first, we recently found out that the numbers in my JPCB 
paper can not be reproduced in 4.0 (embarassingly this was found out 
during a tutorial that I was giving). We are looking into this. Second 
we are busy implementing a new algorithm due to Markovitch * Agmon (JCP 
129 (2008) p. 084505) that has several advantages over the Luzar approach.


Cheers,
--
David.

David van der Spoel, PhD, Professor of Biology
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
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se

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Re: [gmx-users] Interpretation of g_hbond results

2009-02-24 Thread Manik Mayur 
On Tue, Feb 24, 2009 at 9:44 PM, Justin A. Lemkul  wrote:

>
> Hi,
>
> I have a quick question about interpreting the output from g_hbond.  I am
> using the -ac option to calculate H-bond lifetimes between my protein and a
> series of different, bound ligands.  I read the associated paper, but I
> would like to confirm the interpretation of the results before I continue
> much further.  I obtained the following:
>

Which paper are you talking about? Is there a paper for each gromacs
postprocessing tool?

--
> Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
> Forward 0.003309.475  19.590  0.000294756
> Backward0.007136.034  17.471
> One-way 0.002471.990  20.678
> Integral0.001   1534.894  23.717
> Relaxation  0.002606.619  21.325
>
> The "forward" and "backward" rates and times make sense based on equations
> 3 & 4 in the paper, but I could not find an explanation of what "one-way"
> and "relaxation" are.  Is the "integral" value taken from equation 2, and
> thus should be interpreted as the overall H-bond lifetime?
>
> Thanks,
> Justin
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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> gmx-users mailing listgmx-users@gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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> or send it to gmx-users-requ...@gromacs.org.
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>



-- 
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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