Re: [gmx-users] HB lifetime

[Justin A. Lemkul]

Nidhi Katyal wrote:

yes  acf  14477/14477 .


I believe what Erik has been asking is if you have plotted the ACF curve that 
g_hbond produces to see if there is any anomalous behavior.



But rmsd plot did give indication about the convergence.


What RMSD plot?

-Justin


Thank you in advance.

On Fri, Mar 30, 2012 at 4:26 AM, Erik Marklund > wrote:


Ah. -666 is used whenever the sitting of the kinetic model fails to
converge. This is a poor way of signalling that something went wrong
that should be changed. Again, did you *look* at the acf?

Erik

30 mar 2012 kl. 11.53 skrev Nidhi Katyal:


for another system (at 250K) also i have calculated hydrogen bond
lifetime using:
hbond -f *.xtc -s *.tpr -ac *.xvg -num *.xvg -life *.xvg -temp 250
 whose output is :
acf  14477/14477
normalization for c(t)=0.0135742 for gh(t)=6.78702e-05 
hydogen bond thermodynamics at T=250K

fitting parameters chi^2 = 3.89447e-06
Type  rate   time  DG  chi^2
forward  -1.201   -0.833   -666.000   3.89447e-06
backward   -0.354   -2.823   -666.000   
..


Here again i am getting negative hydrogen bond lifetime.
Please suggest me where i am getting wrong and what does negative
lifetime mean?
Thank you in advance.


On Thu, Mar 29, 2012 at 12:56 PM, Erik Marklund
mailto:er...@xray.bmc.uu.se>> wrote:


29 mar 2012 kl. 18.47 skrev Nidhi Katyal:


Dear All
I would like to know the strength of the given bond by
calculating the lifetime of that bond.For the same reason i used:
g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg
-life *.xvg
and i got:
TypeRate(1/ps)  Time(ps)  ...
Forward-0.182-5.495
...
HB lifetime=50.60ps
Note that the lifetime obtained in this manner is close to
useless.Use the -ac option instead and check the forward
lifetime.
..
Will it be correct to say that lifetime is -5.495ps (looking
at forward time)? But then what does negative lifetime implies?
Thanks in advance.


Seems weird. Could the amount of underlying data be
insufficient? Have you looked at the acf?

Erik

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Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se 
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Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se 
http://www2.icm.uu.se/molbio/elflab/index.html


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Re: [gmx-users] HB lifetime

[Nidhi Katyal]

yes  acf  14477/14477 .
But rmsd plot did give indication about the convergence.
Thank you in advance.

On Fri, Mar 30, 2012 at 4:26 AM, Erik Marklund  wrote:

> Ah. -666 is used whenever the sitting of the kinetic model fails to
> converge. This is a poor way of signalling that something went wrong that
> should be changed. Again, did you *look* at the acf?
>
> Erik
>
> 30 mar 2012 kl. 11.53 skrev Nidhi Katyal:
>
> for another system (at 250K) also i have calculated hydrogen bond lifetime
> using:
> hbond -f *.xtc -s *.tpr -ac *.xvg -num *.xvg -life *.xvg -temp 250
>  whose output is :
> acf  14477/14477
> normalization for c(t)=0.0135742 for gh(t)=6.78702e-05
> hydogen bond thermodynamics at T=250K
> fitting parameters chi^2 = 3.89447e-06
> Type  rate   time  DG  chi^2
> forward  -1.201   -0.833   -666.000   3.89447e-06
> backward   -0.354   -2.823   -666.000
> ..
>
> Here again i am getting negative hydrogen bond lifetime.
> Please suggest me where i am getting wrong and what does negative lifetime
> mean?
> Thank you in advance.
>
>
> On Thu, Mar 29, 2012 at 12:56 PM, Erik Marklund wrote:
>
>>
>> 29 mar 2012 kl. 18.47 skrev Nidhi Katyal:
>>
>> Dear All
>> I would like to know the strength of the given bond by calculating the
>> lifetime of that bond.For the same reason i used:
>> g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg -life *.xvg
>>  and i got:
>> TypeRate(1/ps)  Time(ps)  ...
>> Forward-0.182-5.495
>> ...
>> HB lifetime=50.60ps
>> Note that the lifetime obtained in this manner is close to useless.Use
>> the -ac option instead and check the forward lifetime.
>> ..
>> Will it be correct to say that lifetime is -5.495ps (looking at forward
>> time)? But then what does negative lifetime implies?
>> Thanks in advance.
>>
>>
>> Seems weird. Could the amount of underlying data be insufficient? Have
>> you looked at the acf?
>>
>> Erik
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>>
>>  ---
>> Erik Marklund, PhD
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,75124 Uppsala, Sweden
>> phone:+46 18 471 6688fax: +46 18 511 755
>> er...@xray.bmc.uu.se
>> http://www2.icm.uu.se/molbio/elflab/index.html
>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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> ---
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 6688fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
>
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Re: [gmx-users] HB lifetime

[Erik Marklund]

Ah. -666 is used whenever the sitting of the kinetic model fails to converge. 
This is a poor way of signalling that something went wrong that should be 
changed. Again, did you *look* at the acf?

Erik

30 mar 2012 kl. 11.53 skrev Nidhi Katyal:

> for another system (at 250K) also i have calculated hydrogen bond lifetime 
> using:
> hbond -f *.xtc -s *.tpr -ac *.xvg -num *.xvg -life *.xvg -temp 250
>  whose output is :
> acf  14477/14477
> normalization for c(t)=0.0135742 for gh(t)=6.78702e-05 
> hydogen bond thermodynamics at T=250K
> fitting parameters chi^2 = 3.89447e-06
> Type  rate   time  DG  chi^2
> forward  -1.201   -0.833   -666.000   3.89447e-06
> backward   -0.354   -2.823   -666.000   
> ..
> 
> Here again i am getting negative hydrogen bond lifetime.
> Please suggest me where i am getting wrong and what does negative lifetime 
> mean?
> Thank you in advance.
> 
> 
> On Thu, Mar 29, 2012 at 12:56 PM, Erik Marklund  wrote:
> 
> 29 mar 2012 kl. 18.47 skrev Nidhi Katyal:
> 
>> Dear All
>> I would like to know the strength of the given bond by calculating the 
>> lifetime of that bond.For the same reason i used:
>> g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg -life *.xvg
>> and i got:
>> TypeRate(1/ps)  Time(ps)  ...
>> Forward-0.182-5.495
>> ...
>> HB lifetime=50.60ps
>> Note that the lifetime obtained in this manner is close to useless.Use the 
>> -ac option instead and check the forward lifetime.
>> ..
>> Will it be correct to say that lifetime is -5.495ps (looking at forward 
>> time)? But then what does negative lifetime implies?
>> Thanks in advance.
> 
> Seems weird. Could the amount of underlying data be insufficient? Have you 
> looked at the acf?
> 
> Erik
> 
>> -- 
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> ---
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 6688fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
> 
> 
> --
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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Re: [gmx-users] HB lifetime

[Nidhi Katyal]

for another system (at 250K) also i have calculated hydrogen bond lifetime
using:
hbond -f *.xtc -s *.tpr -ac *.xvg -num *.xvg -life *.xvg -temp 250
 whose output is :
acf  14477/14477
normalization for c(t)=0.0135742 for gh(t)=6.78702e-05
hydogen bond thermodynamics at T=250K
fitting parameters chi^2 = 3.89447e-06
Type  rate   time  DG  chi^2
forward  -1.201   -0.833   -666.000   3.89447e-06
backward   -0.354   -2.823   -666.000
..

Here again i am getting negative hydrogen bond lifetime.
Please suggest me where i am getting wrong and what does negative lifetime
mean?
Thank you in advance.


On Thu, Mar 29, 2012 at 12:56 PM, Erik Marklund wrote:

>
> 29 mar 2012 kl. 18.47 skrev Nidhi Katyal:
>
> Dear All
> I would like to know the strength of the given bond by calculating the
> lifetime of that bond.For the same reason i used:
> g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg -life *.xvg
> and i got:
> TypeRate(1/ps)  Time(ps)  ...
> Forward-0.182-5.495
> ...
> HB lifetime=50.60ps
> Note that the lifetime obtained in this manner is close to useless.Use the
> -ac option instead and check the forward lifetime.
> ..
> Will it be correct to say that lifetime is -5.495ps (looking at forward
> time)? But then what does negative lifetime implies?
> Thanks in advance.
>
>
> Seems weird. Could the amount of underlying data be insufficient? Have you
> looked at the acf?
>
> Erik
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> ---
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 6688fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] HB lifetime

[Erik Marklund]

29 mar 2012 kl. 18.47 skrev Nidhi Katyal:

> Dear All
> I would like to know the strength of the given bond by calculating the 
> lifetime of that bond.For the same reason i used:
> g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg -life *.xvg
> and i got:
> TypeRate(1/ps)  Time(ps)  ...
> Forward-0.182-5.495
> ...
> HB lifetime=50.60ps
> Note that the lifetime obtained in this manner is close to useless.Use the 
> -ac option instead and check the forward lifetime.
> ..
> Will it be correct to say that lifetime is -5.495ps (looking at forward 
> time)? But then what does negative lifetime implies?
> Thanks in advance.

Seems weird. Could the amount of underlying data be insufficient? Have you 
looked at the acf?

Erik

> -- 
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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[gmx-users] HB lifetime

[Nidhi Katyal]

Dear All
I would like to know the strength of the given bond by calculating the
lifetime of that bond.For the same reason i used:
g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg -life *.xvg
and i got:
TypeRate(1/ps)  Time(ps)  ...
Forward-0.182-5.495
...
HB lifetime=50.60ps
Note that the lifetime obtained in this manner is close to useless.Use the
-ac option instead and check the forward lifetime.
..
Will it be correct to say that lifetime is -5.495ps (looking at forward
time)? But then what does negative lifetime implies?
Thanks in advance.
-- 
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Re: [gmx-users] HB lifetime

[David van der Spoel]

Christopher Daub wrote:

Hi Omer,

We are aware of your work with Dr. Agmon, and I believe Dr. Luzar has 
spoken with him about it.  I don't understand it enough to say much, but 
I don't think we have substantive disagreements with it.  Of course, the 
questioner was asking about the implementation of the Luzar model in 
Gromacs, so I tried to explain some of the background of her ideas. 
 Perhaps they'll implement your HB model in Gromacs 5...



I would encourage anyone to contribute  implementation of this algorithm 
 to the current g_hbond code. Please get in touch with me off-list if 
you are interested.




Cheers,
Chris.

On Oct 2, 2008, at 4:45 AM, Omer Markovitch wrote:


Please see my comments below.




Hi,

The HB definitions and associated lifetimes are a bit arbitrary,
so there' s always going to be some ambiguity here.  That being
said, the reason the integral of the HB correlation function C(t)
isn't an ideal definition is that C(t) is only roughly
exponential.  Same argument goes for getting the lifetime from a
fit to C(t), or looking for the time where C(t)=1/e, or similar
simple approximations.

 
I disagree. HB lifetime is only slightly dependent on the exact values 
of the geometric parameters, around the usual values of R(O...O)= 3.5 
Angstrom & angle(O...O-H)= 30 degrees, please see JCP 129, 84505 (a 
link to the abstract is given below).
C(t) of a HB obeys the analytical solution of the reversible geminate 
recombination (see a short review in JCP 129), and so its tail follows 
a power law: C(t) ~ Keq*(D*t)^-3/2, which is indicative of a 3 
dimensions diffusion.



What Luzar recommends is to think about an equilibrium between
bound and unbound molecules, so that they interact with a forward
and a backward rate constant k and k'.  k gives the forward rate,
ie. the HB breaking rate, and k' gives the HB reformation rate...
they are not equal due to the diffusion of unbound molecules away
from the solvation shell.  There are a few advantages of going
this route, not the least of which is that you tend to get similar
lifetimes regardless of small changes in the HB definition, and
whether you use geometric or energetic criteria, etc.


The reversible geminate recombination deals with the A+B <---> C, here 
A=B=H2O & C=(H2O)2, the bound water dimer.
From a single fit to C(t) one receives the bimolecular forward & 
backward rate constants, which are well defined.
k' you suggest is an apparent unimolecular rate constant, which 
appears to be more suited for short times.
 



Extracting these rate constants is a bit tricky (I usually do it
by hand), but I guess gromacs has a scheme to do it... I haven't
actually looked at it (though I really should!).  I'd recommend
some caution though, a scheme that works well for HB's between
water molecules in bulk may need to be adjusted to properly model
HB's between water and polar atoms.


I have to disagree again. The A+B=C problem has an analytical 
solution. Technically, ones only need to know how to calculate an 
error-function and to solve a cubic equation, please see eq. 9, 10 at 
JCP 129.
The geminate problem is robust in the sense that it describes C(t) of 
ANY 2 particles, as long as their behavior is controlled by diffusion, 
it describes the water pair, but should describe also, for example, 
liquid argon. For the second case, ofcourse, different rate constants 
are expected.


One should NOT see JCP 129 as a "proof" that previous works were 
absolutly wrong !
Instead, it shows that the postulate by Luzar & Chandler, that C(t) of 
water is controlled by diffusion, is right, and that with the 
analytical solution of the geminate problem one can understand some 
aspects of the water dimer. For example - what causes the activation 
energies of the forward & backward rate constants to be about similar 
rather then being different by the strength of 1 HB?


Hope I was clear.
Omer Markovitch.

** a link to JCP 129, 84505 (2008) http://dx.doi.org/10.1063/1.2968608
** supporting information includes a short trajectory movie





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--
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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
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

Re: [gmx-users] HB lifetime

[Christopher Daub]

Hi Omer,

We are aware of your work with Dr. Agmon, and I believe Dr. Luzar has  
spoken with him about it.  I don't understand it enough to say much,  
but I don't think we have substantive disagreements with it.  Of  
course, the questioner was asking about the implementation of the  
Luzar model in Gromacs, so I tried to explain some of the background  
of her ideas.  Perhaps they'll implement your HB model in Gromacs 5...


Cheers,
Chris.

On Oct 2, 2008, at 4:45 AM, Omer Markovitch wrote:


Please see my comments below.



Hi,

The HB definitions and associated lifetimes are a bit arbitrary, so  
there' s always going to be some ambiguity here.  That being said,  
the reason the integral of the HB correlation function C(t) isn't  
an ideal definition is that C(t) is only roughly exponential.  Same  
argument goes for getting the lifetime from a fit to C(t), or  
looking for the time where C(t)=1/e, or similar simple approximations.


I disagree. HB lifetime is only slightly dependent on the exact  
values of the geometric parameters, around the usual values of R 
(O...O)= 3.5 Angstrom & angle(O...O-H)= 30 degrees, please see JCP  
129, 84505 (a link to the abstract is given below).
C(t) of a HB obeys the analytical solution of the reversible  
geminate recombination (see a short review in JCP 129), and so its  
tail follows a power law: C(t) ~ Keq*(D*t)^-3/2, which is  
indicative of a 3 dimensions diffusion.



What Luzar recommends is to think about an equilibrium between  
bound and unbound molecules, so that they interact with a forward  
and a backward rate constant k and k'.  k gives the forward rate,  
ie. the HB breaking rate, and k' gives the HB reformation rate...  
they are not equal due to the diffusion of unbound molecules away  
from the solvation shell.  There are a few advantages of going this  
route, not the least of which is that you tend to get similar  
lifetimes regardless of small changes in the HB definition, and  
whether you use geometric or energetic criteria, etc.


The reversible geminate recombination deals with the A+B <---> C,  
here A=B=H2O & C=(H2O)2, the bound water dimer.
From a single fit to C(t) one receives the bimolecular forward &  
backward rate constants, which are well defined.
k' you suggest is an apparent unimolecular rate constant, which  
appears to be more suited for short times.



Extracting these rate constants is a bit tricky (I usually do it by  
hand), but I guess gromacs has a scheme to do it... I haven't  
actually looked at it (though I really should!).  I'd recommend  
some caution though, a scheme that works well for HB's between  
water molecules in bulk may need to be adjusted to properly model  
HB's between water and polar atoms.


I have to disagree again. The A+B=C problem has an analytical  
solution. Technically, ones only need to know how to calculate an  
error-function and to solve a cubic equation, please see eq. 9, 10  
at JCP 129.
The geminate problem is robust in the sense that it describes C(t)  
of ANY 2 particles, as long as their behavior is controlled by  
diffusion, it describes the water pair, but should describe also,  
for example, liquid argon. For the second case, ofcourse, different  
rate constants are expected.


One should NOT see JCP 129 as a "proof" that previous works were  
absolutly wrong !
Instead, it shows that the postulate by Luzar & Chandler, that C(t)  
of water is controlled by diffusion, is right, and that with the  
analytical solution of the geminate problem one can understand some  
aspects of the water dimer. For example - what causes the  
activation energies of the forward & backward rate constants to be  
about similar rather then being different by the strength of 1 HB?


Hope I was clear.
Omer Markovitch.

** a link to JCP 129, 84505 (2008) http://dx.doi.org/10.1063/1.2968608
** supporting information includes a short trajectory movie


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Re: [gmx-users] HB lifetime

[Omer Markovitch]

Please see my comments below.

>
> Hi,
>
> The HB definitions and associated lifetimes are a bit arbitrary, so there'
> s always going to be some ambiguity here.  That being said, the reason the
> integral of the HB correlation function C(t) isn't an ideal definition is
> that C(t) is only roughly exponential.  Same argument goes for getting the
> lifetime from a fit to C(t), or looking for the time where C(t)=1/e, or
> similar simple approximations.
>

I disagree. HB lifetime is only slightly dependent on the exact values of
the geometric parameters, around the usual values of R(O...O)= 3.5 Angstrom
& angle(O...O-H)= 30 degrees, please see JCP 129, 84505 (a link to the
abstract is given below).
C(t) of a HB obeys the analytical solution of the reversible geminate
recombination (see a short review in JCP 129), and so its tail follows a
power law: C(t) ~ Keq*(D*t)^-3/2, which is indicative of a 3 dimensions
diffusion.


> What Luzar recommends is to think about an equilibrium between bound and
> unbound molecules, so that they interact with a forward and a backward rate
> constant k and k'.  k gives the forward rate, ie. the HB breaking rate, and
> k' gives the HB reformation rate... they are not equal due to the diffusion
> of unbound molecules away from the solvation shell.  There are a few
> advantages of going this route, not the least of which is that you tend to
> get similar lifetimes regardless of small changes in the HB definition, and
> whether you use geometric or energetic criteria, etc.
>

The reversible geminate recombination deals with the A+B <---> C, here
A=B=H2O & C=(H2O)2, the bound water dimer.
>From a single fit to C(t) one receives the bimolecular forward & backward
rate constants, which are well defined.
k' you suggest is an apparent unimolecular rate constant, which appears to
be more suited for short times.


>
> Extracting these rate constants is a bit tricky (I usually do it by hand),
> but I guess gromacs has a scheme to do it... I haven't actually looked at it
> (though I really should!).  I'd recommend some caution though, a scheme that
> works well for HB's between water molecules in bulk may need to be adjusted
> to properly model HB's between water and polar atoms.
>

I have to disagree again. The A+B=C problem has an analytical solution.
Technically, ones only need to know how to calculate an error-function and
to solve a cubic equation, please see eq. 9, 10 at JCP 129.
The geminate problem is robust in the sense that it describes C(t) of ANY 2
particles, as long as their behavior is controlled by diffusion, it
describes the water pair, but should describe also, for example, liquid
argon. For the second case, ofcourse, different rate constants are expected.

One should NOT see JCP 129 as a "proof" that previous works were absolutly
wrong !
Instead, it shows that the postulate by Luzar & Chandler, that C(t) of water
is controlled by diffusion, is right, and that with the analytical solution
of the geminate problem one can understand some aspects of the water dimer.
For example - what causes the activation energies of the forward & backward
rate constants to be about similar rather then being different by the
strength of 1 HB?

Hope I was clear.
Omer Markovitch.

** a link to JCP 129, 84505 (2008) http://dx.doi.org/10.1063/1.2968608
** supporting information includes a short trajectory movie
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[gmx-users] HB lifetime

[Christopher Daub]

From: Laercio Pol Fachin <[EMAIL PROTECTED]>
Date: September 30, 2008 9:50:48 AM EDT
To: gmx-users@gromacs.org
Subject: [gmx-users] Hydrogen Bond Lifetime
Reply-To: [EMAIL PROTECTED], Discussion list for GROMACS  
users 



Hi, all.

I am analyzing the hydrogen bond lifetime of water molecules around  
polar atoms of my molecule. However, I have faced different HB  
lifetime definitions in different sources. A sample of what I  
obtained employing g_hbond is below:


"g_hbond -f .xtc -s .tpr -n .ndx -ac .xvg -b 0 -e 1"

Type  Rate (1/ps)  Time (ps)  DG (kJ/mol)
Forward 0.797  1.254   5.089
Backward0.061 16.475  11.474
One-way 1.323  0.756   3.835
Integral0.948  1.055   4.661
Relaxation  2.195  0.456   2.579

# In GROMACS 3.3 manual, page 171, it is said that "the integral of  
C(t) gives a rough estimate of the average H-bond lifetime", which  
points to a HB lifetime of 1.055 ps (right?);
# On the other hand, in previous discussion in this list, I have  
found that "according to Luzar the time corresponding to the  
forward rate constant should be regarded as 'the' hbond lifetime",  
which points to a HB lifetime of 0.797;


Can anyone please clarify such points?



Hi,

The HB definitions and associated lifetimes are a bit arbitrary, so  
there' s always going to be some ambiguity here.  That being said,  
the reason the integral of the HB correlation function C(t) isn't an  
ideal definition is that C(t) is only roughly exponential.  Same  
argument goes for getting the lifetime from a fit to C(t), or looking  
for the time where C(t)=1/e, or similar simple approximations.


What Luzar recommends is to think about an equilibrium between bound  
and unbound molecules, so that they interact with a forward and a  
backward rate constant k and k'.  k gives the forward rate, ie. the  
HB breaking rate, and k' gives the HB reformation rate... they are  
not equal due to the diffusion of unbound molecules away from the  
solvation shell.  There are a few advantages of going this route, not  
the least of which is that you tend to get similar lifetimes  
regardless of small changes in the HB definition, and whether you use  
geometric or energetic criteria, etc.


Extracting these rate constants is a bit tricky (I usually do it by  
hand), but I guess gromacs has a scheme to do it... I haven't  
actually looked at it (though I really should!).  I'd recommend some  
caution though, a scheme that works well for HB's between water  
molecules in bulk may need to be adjusted to properly model HB's  
between water and polar atoms.


So in this case, the "best" rate constant is probably 0.797 ps-1 or a  
time of 1.254 ps, which is only a bit slower than in bulk water.  I'm  
very surprised that the backward rate constant is so small though...  
this is about 1 ps-1 in bulk water! I've never seen k'  be this small...


Exhaustive details about the HB dynamics issues can be found eg. here:

A. Luzar, JCP 113, 10663 (2000)

Hope this helps,
Chris Daub
(currently postdoc with Dr. Luzar).___
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Re: [gmx-users] HB lifetime in g_hbond

[David van der Spoel]

Patricia Soto Becerra wrote:

Hi,
I have a question regarding the calculation of hydrogen bond lifetimes 
in g_hbond:


Line 1094 of gmx_hbond.c v 1.16.2.11 2006/04/02 (which is equivalent to 
line 1121 of gmx_hbond.c v 1.28 2006/08/30) reads:


t  = hb->time[i] - hb->time[0] - 0.5*dt;

leading to the time series 1, 3, 5,.. that does not correspond to my 
sampling frequency of 2ps. This affects the calculation of x1 in the 
immediate next line. My question is: Why is t defined in this way?


The program computes an histogram and centers the points in between time 
points. Note that this flag gives you useless lifetimes, see J. Phys. 
Chem. B 110 pp. 4393-4398 (2006). You want to use the lifetime that 
comes from the -ac option (look at line with Forward)


--
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
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] HB lifetime in g_hbond

[Patricia Soto Becerra]

Hi,
I have a question regarding the calculation of hydrogen bond lifetimes in 
g_hbond:


Line 1094 of gmx_hbond.c v 1.16.2.11 2006/04/02 (which is equivalent to 
line 1121 of gmx_hbond.c v 1.28 2006/08/30) reads:


t  = hb->time[i] - hb->time[0] - 0.5*dt;

leading to the time series 1, 3, 5,.. that does not correspond to my 
sampling frequency of 2ps. This affects the calculation of x1 in the 
immediate next line. My question is: Why is t defined in this way?


This question was posted in the past but did not find answer in the users 
list.


Thanks!

Patricia
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