Re: [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

[Erik Marklund]

Dear Apramita,

Right. Still, the same still applies with regards to the -666.

It could be a matter of statistics, why you get sensible values for the longer 
trajectory chunk. Also, note that the trajectory length limits the possible 
timescales that the model can tease out. If I understand correctly, your 
trajectories with and without pic have different length, so I’m not surprised 
that the kinetic constants that you get out are different.

Kind regards,
Erik

__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 29 Aug 2017, at 14:02, Apramita Chand 
> wrote:

Dear Eric,
Its actually the DG(kj/mol) value  which is -666. The time is coming to
be-126 ps. But the g_hbond is failing to fit the kinetic model to the data
for the last 60ns as you have implied. Any reasons why this could have
happened, while for the entire trajectory, I am getting positive values?
But for the entire trajectory, with and without pbc(1793ps and 2345ps
respectively) , I have two separate values for lifetime. Which one should I
take?

I would be appreciative of any suggestions

Looking forward to your help,

yours sincerely
Apramita

















*Message:( 2 Date: Tue, 29 Aug 2017 08:09:32 + From: Erik Marklund
 
>> To:
"gmx-us...@gromacs.org 
>" 

>> Subject: Re: [gmx-users] 
Difference in Hydrogen
Bond Lifetimes on truncating trajectory and also on using pbc
Message-ID: 

>>
 Content-Type:
text/plain; charset="utf-8" Dear Apramita, IIRC, the time is set to.-666
when gmx hbond fails to fit the kinetic model to the data. Not the most
informative way of indicating an error perhaps. Kind regards, Erik
__*



* Erik Marklund, PhD, Marie Sk?odowska Curie INCA Fellow
Department of Chemistry ? BMC, Uppsala University +46 (0)18 471 4539
erik.markl...@kemi.uu.se 
><*

*mailto:erik.markl...@kemi.uu.se 
>> On 29 Aug
2017, at 07:20, Apramita Chand 

><*



















*mailto:apramita.ch...@gmail.com 

Re: [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

[Apramita Chand]

Dear Eric,
Its actually the DG(kj/mol) value  which is -666. The time is coming to
be-126 ps. But the g_hbond is failing to fit the kinetic model to the data
for the last 60ns as you have implied. Any reasons why this could have
happened, while for the entire trajectory, I am getting positive values?
But for the entire trajectory, with and without pbc(1793ps and 2345ps
respectively) , I have two separate values for lifetime. Which one should I
take?

I would be appreciative of any suggestions

Looking forward to your help,

yours sincerely
Apramita

















*Message:( 2 Date: Tue, 29 Aug 2017 08:09:32 + From: Erik Marklund
> To:
"gmx-us...@gromacs.org " > Subject: Re: [gmx-users] Difference in Hydrogen
Bond Lifetimes on truncating trajectory and also on using pbc
Message-ID: > Content-Type:
text/plain; charset="utf-8" Dear Apramita, IIRC, the time is set to.-666
when gmx hbond fails to fit the kinetic model to the data. Not the most
informative way of indicating an error perhaps. Kind regards, Erik
__*



* Erik Marklund, PhD, Marie Sk?odowska Curie INCA Fellow
Department of Chemistry ? BMC, Uppsala University +46 (0)18 471 4539
erik.markl...@kemi.uu.se <*

*mailto:erik.markl...@kemi.uu.se > On 29 Aug
2017, at 07:20, Apramita Chand <*



















*mailto:apramita.ch...@gmail.com >> wrote: Dear
All, I've carried out a 100ns simulation of protein in water and want to
calculate hydrogen bond (forward) lifetime between Protein-Water.
Initially, I thought it would be better to analyse hydrogen bonds in last
60ns of simulation, so I truncated the trajectory using g_trjconv using -b
4 -e 10 as options. The results came as *ACF
10628/10628Normalization for c(t) = 0.0621737 for gh(t) = 2.07246e-06Back
Off! I just backed up hbac1.xvg to ./#hbac1.xvg.1#Hydrogen bond
thermodynamics at T = 300 KFitting parameters chi^2 = 2.8733Q =
  0-*


























*-Type Rate (1/ps) Time (ps)  DG (kJ/mol)
Chi^2Forward-0.008 -126.851-666.000  2.8733* (This came for
both with and without pbc). I also tried to do it from the g_hbond command
itself by giving starting time as 40ns and ending as 100ns, but again it
came negative lifetime. Next, I tried g_trjconv with application of -pbc
mol -ur compact options on untruncated(100ns) trajectory. The results came
as: *ACF 11303/11303Normalization for c(t) = 0.0615891 for gh(t) =
1.23179e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.2#Hydrogen
bond thermodynamics at T = 300 KFitting parameters chi^2 =3.03095Q =
  0-*




















*-Type Rate (1/ps) Time (ps)  DG (kJ/mol)
Chi^2Forward 0.001 1793.775  23.259 3.03095* When I tried
the same with the original unconverted trajectory(without g_trjconv
,without pbc options), I got a lifetime of *2345.890ps*. *My question is
,1) why do the truncated trajectories give negative values for my
simulation?* *2)If I take the whole 100ns for analysis of hydrogen bond
lifetime, which value should I take, since application of pbc gives a
different value than that of the original trajectory value of lifetime.* I
would be very grateful for your help. Looking forward to your suggestions
Yours sincerely Apramita Chand*
-- 
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

[Apramita Chand]

Dear All,
I've carried out a 100ns simulation of protein in water and want to
calculate hydrogen bond (forward) lifetime between Protein-Water.
Initially, I thought it would be better to analyse hydrogen bonds in last
60ns of simulation, so I truncated the trajectory using g_trjconv using -b
4 -e 10 as options. The results came as









*ACF 10628/10628Normalization for c(t) = 0.0621737 for gh(t) =
2.07246e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.1#Hydrogen
bond thermodynamics at T = 300 KFitting parameters chi^2 = 2.8733Q
=  0--Type
Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2Forward-0.008
-126.851-666.000  2.8733*

(This came for both with and without pbc). I also tried to do it from the
g_hbond command itself by giving starting time as 40ns and ending as 100ns,
but again it came negative lifetime.


Next, I tried g_trjconv with application of -pbc mol -ur compact options on
untruncated(100ns) trajectory. The results came as:













*ACF 11303/11303Normalization for c(t) = 0.0615891 for gh(t) =
1.23179e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.2#Hydrogen
bond thermodynamics at T = 300 KFitting parameters chi^2 =3.03095Q
=  0--Type
Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2Forward 0.001
1793.775  23.259 3.03095*
When I tried the same with the original unconverted trajectory(without
g_trjconv ,without pbc options), I got a lifetime of *2345.890ps*.






*My question is ,1) why do the truncated trajectories give negative values
for my simulation?*



*2)If I take the whole 100ns for analysis of hydrogen bond lifetime, which
value should I take, since application of pbc gives a different value than
that of the original trajectory value of lifetime.*
I would be very grateful for your help.
Looking forward to your suggestions


Yours sincerely
Apramita Chand
-- 
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.