Re: [gmx-users] g_hbond and contact

[Kavyashree M]

Thank you Sir.

On Tue, Mar 5, 2013 at 4:33 PM, Erik Marklund  wrote:

>
> On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote:
>
>  Sir,
>>
>> I used gromacs 4.6. I got the point - index file will tell how many
>> contacts an
>> atom has made during the trajectory. Whether it has made a contact with an
>> atom only in once or all the time, in the whole trajectory, it will be
>> mentioned.
>> Am I right?
>>
>
> Yes.
>
>
>
>> So from the problem I had, can I say that no. of contact/atom had
>> increased
>> in S2 while the no. of contact/time decreased?
>>
>
> That depends. If 'contact' means unique interactions and 'atom' means e.g.
> all atoms in in your system, then yes.
>
>
>> Its a bit confusing though!
>>
>> Thank you
>> kavya
>>
>> On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund 
>> wrote:
>>
>>  To clarify: the -hbn output is not very indicative of how many contacts
>>> there were since some of them could be present in one frame but absent in
>>> 99. The -num option, however, provides the number of contacts over
>>> time, and its time average probably tells you much more in this case.
>>>
>>> What version of g_hbond are you using? I remember there were several
>>> bugfixes over the last 6 months or so. With the latest version(s) I
>>> believe
>>> that the -merge flag has no effect on contact analysis, which is correct.
>>>
>>> Erik
>>>
>>>
>>>  --
>> gmx-users mailing listgmx-users@gromacs.org
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>
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Re: [gmx-users] g_hbond and contact

[Erik Marklund]

On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote:


Sir,

I used gromacs 4.6. I got the point - index file will tell how many
contacts an
atom has made during the trajectory. Whether it has made a contact  
with an

atom only in once or all the time, in the whole trajectory, it will be
mentioned.
Am I right?


Yes.



So from the problem I had, can I say that no. of contact/atom had  
increased

in S2 while the no. of contact/time decreased?


That depends. If 'contact' means unique interactions and 'atom' means  
e.g. all atoms in in your system, then yes.




Its a bit confusing though!

Thank you
kavya

On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund   
wrote:


To clarify: the -hbn output is not very indicative of how many  
contacts
there were since some of them could be present in one frame but  
absent in
99. The -num option, however, provides the number of contacts  
over

time, and its time average probably tells you much more in this case.

What version of g_hbond are you using? I remember there were several
bugfixes over the last 6 months or so. With the latest version(s) I  
believe
that the -merge flag has no effect on contact analysis, which is  
correct.


Erik



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Re: [gmx-users] g_hbond and contact

[Kavyashree M]

Sir,

I used gromacs 4.6. I got the point - index file will tell how many
contacts an
atom has made during the trajectory. Whether it has made a contact with an
atom only in once or all the time, in the whole trajectory, it will be
mentioned.
Am I right?

So from the problem I had, can I say that no. of contact/atom had increased
in S2 while the no. of contact/time decreased?

Its a bit confusing though!

Thank you
kavya

On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund  wrote:

> To clarify: the -hbn output is not very indicative of how many contacts
> there were since some of them could be present in one frame but absent in
> 99. The -num option, however, provides the number of contacts over
> time, and its time average probably tells you much more in this case.
>
> What version of g_hbond are you using? I remember there were several
> bugfixes over the last 6 months or so. With the latest version(s) I believe
> that the -merge flag has no effect on contact analysis, which is correct.
>
> Erik
>
>
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Re: [gmx-users] g_hbond and contact

[Erik Marklund]

To clarify: the -hbn output is not very indicative of how many  
contacts there were since some of them could be present in one frame  
but absent in 99. The -num option, however, provides the number of  
contacts over time, and its time average probably tells you much more  
in this case.


What version of g_hbond are you using? I remember there were several  
bugfixes over the last 6 months or so. With the latest version(s) I  
believe that the -merge flag has no effect on contact analysis, which  
is correct.


Erik

On Mar 5, 2013, at 5:20 AM, Kavyashree M wrote:

I am sorry There is no "7ws" Its a typographic error. What I wanted  
to ask

was -
I am comparing two simulations S1 and S2 for contacts at a given cut  
off

I used g_mdmat and g_hbond to calculate it.
g_hbond outputs: of "-num" and "-hbn" was considered.
   1. -hbn output was analysed to calculate how many  
contacts each

   atom has from both  S1 and S2.
   2. -num output graph was compared from both S1 and S2.
g_mdmat output: of "-no" was considered.
   3. -no output was analysed from both S1 and S2 using the
   third column or the second Y value which gives total
contacts
   of each atom.

It was observed that "1" and "3" matched exactly giving the same  
number of

contacts each atom has (in the whole simulations). indicating that the
number
of contacts each atom has was more in S2 than S1.

But the graph from "2" indicated that the number of contacts (along  
the

trajectory)
in S1 was higher than S2.

My doubt is:
The number of contact per atom follows S2 > S1
while number of contacts per time follows S1 > S2.
I am unclear as to what I  have to conclude from this observations.

-> I used the same cutoff throughout.
-> There has not been any swapping of the trajectory while  
analysing.


Thank you
Kavya


On Tue, Mar 5, 2013 at 1:09 AM, Justin Lemkul  wrote:




On 3/4/13 1:10 PM, Kavyashree M wrote:

On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul   
wrote:



When measuring contacts, you don't measure one group, you measure  
the
number of contacts that occur between groups A and B, which  
considers all

atoms in those two groups.



I gave a group of hydrophobic atoms in both cases
The command I gave -
g_hbond_46  -fx.xtc-s   x.tpr-contact   -n   x.ndx   - 
r   0.4

-hbm   o.xpm   -hbn   o.ndx   -num   o.xvg
my index file contained a group of hydrophobic atoms. which I  
supplied in

the x.ndx.



 You don't define contacts in an index group, you define atoms  
that may

or
may not make contacts with others.


The one I mentioned here is the output index file from the  
g_hbond (4.6

version) - o.ndx.




 [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_***
*CZ2_CZ3_CH2

]

   5  7ws
   5 10
   5 14
   5 18
   5 22
   5 24
   5 27
   5 30
   5 35
   5292
   5296
   530


There's something very wrong with this index file.  How did you

generate
it? The presence of a repeated atom number (5) and a nonsensical  
one

(7ws)
leads me to believe that you've done something incorrect.  Did  
this come
from g_hbond? It looks like the output of -hbn, which is only  
useful for

decoding hbmap.xpm, nothing else.


I did not generate this. The tool (g_hbond) generated this index  
file.

It
is the -hbn output.



OK, then I still don't know what "7ws" is, but the only purpose for  
this

file is to provide a key to the existence matrix in hbmap.xpm.  Your
previous description indicated that you were using it for some other
analysis, which would not be appropriate.

The other thing worth mentioning here is something that was posted  
to the
list just a few hours ago, that the output of g_hbond -contact may  
not
agree with other methods of calculating contacts, especially in the  
case of

-merge vs. -nomerge.

-Justin



 From this second section Total contacts was extracted for each  
atom and





compared with

that from a second simulation.
These contacts was matching with the contacts of the 3rd column  
from

g_mdmat output -
@ legend string 0 "Total/mean"
@ legend string 1 "Total"
@ legend string 2 "Mean"
@ legend string 3 "# atoms"
@ legend string 4 "Mean/# atoms"
#resratio  tot  mean  natm  mean/atm
   1 1.001   1110.991110.991
   2 1.244   10 8.0411 8.041
   3 1.166   1311.147111.147
   4 1.036   1110.615110.615


While the time dependent contacts in the xvg file shows that the  
first

simulation has more
contacts than the second one..


That shouldn't be unexpected.  Two independent simulations have no
guarantee of doing the same thing, that's why sampling is so  
important.




Thank you
kavya



--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 

Re: [gmx-users] g_hbond and contact

[Kavyashree M]

I am sorry There is no "7ws" Its a typographic error. What I wanted to ask
was -
I am comparing two simulations S1 and S2 for contacts at a given cut off
I used g_mdmat and g_hbond to calculate it.
g_hbond outputs: of "-num" and "-hbn" was considered.
1. -hbn output was analysed to calculate how many contacts each
atom has from both  S1 and S2.
2. -num output graph was compared from both S1 and S2.
g_mdmat output: of "-no" was considered.
3. -no output was analysed from both S1 and S2 using the
third column or the second Y value which gives total
contacts
of each atom.

It was observed that "1" and "3" matched exactly giving the same number of
contacts each atom has (in the whole simulations). indicating that the
number
of contacts each atom has was more in S2 than S1.

But the graph from "2" indicated that the number of contacts (along the
trajectory)
in S1 was higher than S2.

My doubt is:
The number of contact per atom follows S2 > S1
while number of contacts per time follows S1 > S2.
I am unclear as to what I  have to conclude from this observations.

-> I used the same cutoff throughout.
-> There has not been any swapping of the trajectory while analysing.

Thank you
Kavya


On Tue, Mar 5, 2013 at 1:09 AM, Justin Lemkul  wrote:

>
>
> On 3/4/13 1:10 PM, Kavyashree M wrote:
>
>> On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul  wrote:
>>
>>
>>> When measuring contacts, you don't measure one group, you measure the
>>> number of contacts that occur between groups A and B, which considers all
>>> atoms in those two groups.
>>>
>>>
>> I gave a group of hydrophobic atoms in both cases
>> The command I gave -
>> g_hbond_46  -fx.xtc-s   x.tpr-contact   -n   x.ndx   -r   0.4
>> -hbm   o.xpm   -hbn   o.ndx   -num   o.xvg
>> my index file contained a group of hydrophobic atoms. which I supplied in
>> the x.ndx.
>>
>>
>>
>>>   You don't define contacts in an index group, you define atoms that may
>>> or
>>> may not make contacts with others.
>>>
>>>
>>>  The one I mentioned here is the output index file from the g_hbond (4.6
>> version) - o.ndx.
>>
>>
>>
>>>   [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_***
>>> *CZ2_CZ3_CH2
>>>
>>>  ]
 5  7ws
 5 10
 5 14
 5 18
 5 22
 5 24
 5 27
 5 30
 5 35
 5292
 5296
 530


  There's something very wrong with this index file.  How did you
>>> generate
>>> it? The presence of a repeated atom number (5) and a nonsensical one
>>> (7ws)
>>> leads me to believe that you've done something incorrect.  Did this come
>>> from g_hbond? It looks like the output of -hbn, which is only useful for
>>> decoding hbmap.xpm, nothing else.
>>>
>>>
>>>  I did not generate this. The tool (g_hbond) generated this index file.
>> It
>> is the -hbn output.
>>
>>
>>
> OK, then I still don't know what "7ws" is, but the only purpose for this
> file is to provide a key to the existence matrix in hbmap.xpm.  Your
> previous description indicated that you were using it for some other
> analysis, which would not be appropriate.
>
> The other thing worth mentioning here is something that was posted to the
> list just a few hours ago, that the output of g_hbond -contact may not
> agree with other methods of calculating contacts, especially in the case of
> -merge vs. -nomerge.
>
> -Justin
>
>
>
>>>   From this second section Total contacts was extracted for each atom and
>>>

>  compared with
 that from a second simulation.
 These contacts was matching with the contacts of the 3rd column from
 g_mdmat output -
 @ legend string 0 "Total/mean"
 @ legend string 1 "Total"
 @ legend string 2 "Mean"
 @ legend string 3 "# atoms"
 @ legend string 4 "Mean/# atoms"
 #resratio  tot  mean  natm  mean/atm
 1 1.001   1110.991110.991
 2 1.244   10 8.0411 8.041
 3 1.166   1311.147111.147
 4 1.036   1110.615110.615


 While the time dependent contacts in the xvg file shows that the first
 simulation has more
 contacts than the second one..


  That shouldn't be unexpected.  Two independent simulations have no
>>> guarantee of doing the same thing, that's why sampling is so important.
>>>
>>>
>> Thank you
>> kavya
>>
>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> 

Re: [gmx-users] g_hbond and contact

[Justin Lemkul]

On 3/4/13 1:10 PM, Kavyashree M wrote:

On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul  wrote:



When measuring contacts, you don't measure one group, you measure the
number of contacts that occur between groups A and B, which considers all
atoms in those two groups.



I gave a group of hydrophobic atoms in both cases
The command I gave -
g_hbond_46  -fx.xtc-s   x.tpr-contact   -n   x.ndx   -r   0.4
-hbm   o.xpm   -hbn   o.ndx   -num   o.xvg
my index file contained a group of hydrophobic atoms. which I supplied in
the x.ndx.




  You don't define contacts in an index group, you define atoms that may or
may not make contacts with others.



The one I mentioned here is the output index file from the g_hbond (4.6
version) - o.ndx.




  [ contacts_C_CA_CB_CD_CD1_CD2_**CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_**CZ2_CZ3_CH2

]
5  7ws
5 10
5 14
5 18
5 22
5 24
5 27
5 30
5 35
5292
5296
530



There's something very wrong with this index file.  How did you generate
it? The presence of a repeated atom number (5) and a nonsensical one (7ws)
leads me to believe that you've done something incorrect.  Did this come
from g_hbond? It looks like the output of -hbn, which is only useful for
decoding hbmap.xpm, nothing else.



I did not generate this. The tool (g_hbond) generated this index file. It
is the -hbn output.




OK, then I still don't know what "7ws" is, but the only purpose for this file is 
to provide a key to the existence matrix in hbmap.xpm.  Your previous 
description indicated that you were using it for some other analysis, which 
would not be appropriate.


The other thing worth mentioning here is something that was posted to the list 
just a few hours ago, that the output of g_hbond -contact may not agree with 
other methods of calculating contacts, especially in the case of -merge vs. 
-nomerge.


-Justin



  From this second section Total contacts was extracted for each atom and



compared with
that from a second simulation.
These contacts was matching with the contacts of the 3rd column from
g_mdmat output -
@ legend string 0 "Total/mean"
@ legend string 1 "Total"
@ legend string 2 "Mean"
@ legend string 3 "# atoms"
@ legend string 4 "Mean/# atoms"
#resratio  tot  mean  natm  mean/atm
1 1.001   1110.991110.991
2 1.244   10 8.0411 8.041
3 1.166   1311.147111.147
4 1.036   1110.615110.615


While the time dependent contacts in the xvg file shows that the first
simulation has more
contacts than the second one..



That shouldn't be unexpected.  Two independent simulations have no
guarantee of doing the same thing, that's why sampling is so important.



Thank you
kavya



--


Justin A. Lemkul, Ph.D.
Research Scientist
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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* Please search the archive at 
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Re: [gmx-users] g_hbond and contact

[Kavyashree M]

On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul  wrote:

>
> When measuring contacts, you don't measure one group, you measure the
> number of contacts that occur between groups A and B, which considers all
> atoms in those two groups.
>

I gave a group of hydrophobic atoms in both cases
The command I gave -
g_hbond_46  -fx.xtc-s   x.tpr-contact   -n   x.ndx   -r   0.4
-hbm   o.xpm   -hbn   o.ndx   -num   o.xvg
my index file contained a group of hydrophobic atoms. which I supplied in
the x.ndx.


>
>  You don't define contacts in an index group, you define atoms that may or
> may not make contacts with others.
>
>
The one I mentioned here is the output index file from the g_hbond (4.6
version) - o.ndx.


>
>  [ contacts_C_CA_CB_CD_CD1_CD2_**CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_**CZ2_CZ3_CH2
>> ]
>>5  7ws
>>5 10
>>5 14
>>5 18
>>5 22
>>5 24
>>5 27
>>5 30
>>5 35
>>5292
>>5296
>>530
>>
>>
> There's something very wrong with this index file.  How did you generate
> it? The presence of a repeated atom number (5) and a nonsensical one (7ws)
> leads me to believe that you've done something incorrect.  Did this come
> from g_hbond? It looks like the output of -hbn, which is only useful for
> decoding hbmap.xpm, nothing else.
>
>
I did not generate this. The tool (g_hbond) generated this index file. It
is the -hbn output.


>
>  From this second section Total contacts was extracted for each atom and
>>>
>> compared with
>> that from a second simulation.
>> These contacts was matching with the contacts of the 3rd column from
>> g_mdmat output -
>> @ legend string 0 "Total/mean"
>> @ legend string 1 "Total"
>> @ legend string 2 "Mean"
>> @ legend string 3 "# atoms"
>> @ legend string 4 "Mean/# atoms"
>> #resratio  tot  mean  natm  mean/atm
>>1 1.001   1110.991110.991
>>2 1.244   10 8.0411 8.041
>>3 1.166   1311.147111.147
>>4 1.036   1110.615110.615
>>
>>
>> While the time dependent contacts in the xvg file shows that the first
>> simulation has more
>> contacts than the second one..
>>
>>
> That shouldn't be unexpected.  Two independent simulations have no
> guarantee of doing the same thing, that's why sampling is so important.
>

Thank you
kavya
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Re: [gmx-users] g_hbond and contact

[Justin Lemkul]

On 3/4/13 12:04 PM, Kavyashree M wrote:

Sir,


From Index file which gives the unique contacts -

First section the list of atoms I want to analyse


When measuring contacts, you don't measure one group, you measure the number of 
contacts that occur between groups A and B, which considers all atoms in those 
two groups.



[ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]

second section : the unique contacts of each atoms with others


You don't define contacts in an index group, you define atoms that may or may 
not make contacts with others.



[ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]
   5  7ws
   5 10
   5 14
   5 18
   5 22
   5 24
   5 27
   5 30
   5 35
   5292
   5296
   530



There's something very wrong with this index file.  How did you generate it? 
The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me 
to believe that you've done something incorrect.  Did this come from g_hbond? 
It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, 
nothing else.



From this second section Total contacts was extracted for each atom and

compared with
that from a second simulation.
These contacts was matching with the contacts of the 3rd column from
g_mdmat output -
@ legend string 0 "Total/mean"
@ legend string 1 "Total"
@ legend string 2 "Mean"
@ legend string 3 "# atoms"
@ legend string 4 "Mean/# atoms"
#resratio  tot  mean  natm  mean/atm
   1 1.001   1110.991110.991
   2 1.244   10 8.0411 8.041
   3 1.166   1311.147111.147
   4 1.036   1110.615110.615


While the time dependent contacts in the xvg file shows that the first
simulation has more
contacts than the second one..



That shouldn't be unexpected.  Two independent simulations have no guarantee of 
doing the same thing, that's why sampling is so important.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] g_hbond and contact

[Kavyashree M]

Sir,

>From Index file which gives the unique contacts -
First section the list of atoms I want to analyse
[ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]

second section : the unique contacts of each atoms with others
[ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]
  5  7ws
  5 10
  5 14
  5 18
  5 22
  5 24
  5 27
  5 30
  5 35
  5292
  5296
  530

>From this second section Total contacts was extracted for each atom and
compared with
that from a second simulation.
These contacts was matching with the contacts of the 3rd column from
g_mdmat output -
@ legend string 0 "Total/mean"
@ legend string 1 "Total"
@ legend string 2 "Mean"
@ legend string 3 "# atoms"
@ legend string 4 "Mean/# atoms"
#resratio  tot  mean  natm  mean/atm
  1 1.001   1110.991110.991
  2 1.244   10 8.0411 8.041
  3 1.166   1311.147111.147
  4 1.036   1110.615110.615


While the time dependent contacts in the xvg file shows that the first
simulation has more
contacts than the second one..

I hope I am clear this time.

Thank you
kavya

On Mon, Mar 4, 2013 at 10:05 PM, Justin Lemkul  wrote:

>
>
> On 3/4/13 11:25 AM, Kavyashree M wrote:
>
>> Dear users,
>>
>> I used the following tool for finding the contacts
>> g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn
>> a.ndx
>> -num a.xvg
>>
>>> From the index file, the number of contacts of each atom was extracted.
>>>
>> This and the
>> xvg output was compared with another simulation.
>> It was found that the number of contacts was more in 2nd simulation
>> compared to
>> the first. But When I compared xvg file it was showing the opposite
>> behaviour.
>>
>
> These statements don't make any sense.  How did you determine that the
> number of contacts in simulation 2 was greater than simulation 1, but then
> the .xvg files showed the opposite?  The number of contacts come from the
> .xvg files?  Perhaps you simply swapped your files during analysis.
>
>
>  The contacts was also calculated using g_mdmat for the same cutoff and it
>> was agreeing
>> with the numbers I got from in index output of g_hbond.
>>
>> Why is this difference in index and xvg output?
>>
>
> An index group is a list of atom numbers.  The .xvg output is whatever you
> tell it to be, in this case, the number of contacts within the group
> selected.
>
> -Justin
>
>
>  Also the xvg file looks like -
>>
>> s0 legend "Contacts"
>> @ s1 legend "Pairs within 0.4 nm"
>>40007496   0
>>40027513   0
>>40047605   0
>>40067531   0
>>40087573   0
>>40107546   0
>>40127544   0
>>40147526   0
>>40167530   0
>>40187496   0
>>40207526   0
>> ..
>>
>>
>> Thank you
>> kavya
>>
>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
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> * Please search the archive at http://www.gromacs.org/**
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Re: [gmx-users] g_hbond and contact

[Justin Lemkul]

On 3/4/13 11:25 AM, Kavyashree M wrote:

Dear users,

I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx
-num a.xvg

From the index file, the number of contacts of each atom was extracted.

This and the
xvg output was compared with another simulation.
It was found that the number of contacts was more in 2nd simulation
compared to
the first. But When I compared xvg file it was showing the opposite
behaviour.


These statements don't make any sense.  How did you determine that the number of 
contacts in simulation 2 was greater than simulation 1, but then the .xvg files 
showed the opposite?  The number of contacts come from the .xvg files?  Perhaps 
you simply swapped your files during analysis.



The contacts was also calculated using g_mdmat for the same cutoff and it
was agreeing
with the numbers I got from in index output of g_hbond.

Why is this difference in index and xvg output?


An index group is a list of atom numbers.  The .xvg output is whatever you tell 
it to be, in this case, the number of contacts within the group selected.


-Justin


Also the xvg file looks like -

s0 legend "Contacts"
@ s1 legend "Pairs within 0.4 nm"
   40007496   0
   40027513   0
   40047605   0
   40067531   0
   40087573   0
   40107546   0
   40127544   0
   40147526   0
   40167530   0
   40187496   0
   40207526   0
..


Thank you
kavya



--


Justin A. Lemkul, Ph.D.
Research Scientist
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] g_hbond and contact

[Kavyashree M]

Dear users,

I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx
-num a.xvg
>From the index file, the number of contacts of each atom was extracted.
This and the
xvg output was compared with another simulation.
It was found that the number of contacts was more in 2nd simulation
compared to
the first. But When I compared xvg file it was showing the opposite
behaviour.
The contacts was also calculated using g_mdmat for the same cutoff and it
was agreeing
with the numbers I got from in index output of g_hbond.

Why is this difference in index and xvg output?
Also the xvg file looks like -

s0 legend "Contacts"
@ s1 legend "Pairs within 0.4 nm"
  40007496   0
  40027513   0
  40047605   0
  40067531   0
  40087573   0
  40107546   0
  40127544   0
  40147526   0
  40167530   0
  40187496   0
  40207526   0
..


Thank you
kavya
-- 
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