subject:"\[gmx\-users\] g

Re: [gmx-users] g_hbond problems

2017-03-10 Thread Justin Lemkul




On 3/10/17 4:51 AM, andrea.cor...@unina.it wrote:



I am trying to analyze the hydrogen bonds of my simulations by g_hbond.
I am using an index file where  I created two groups: one with acceptor atoms
(carboxylic oxygen atoms in my structure) and another group with the water
molecules.

I got a segmentation fault with the message:


Select a group: 6
Selected 6: 'PEI_&_OC'
Select a group: 3
Selected 3: 'Water'
Checking for overlap in atoms between PEI_&_OC and Water
Calculating hydrogen bonds between PEI_&_OC (1296 atoms) and Water (258 atoms)
Found 86 donors and 1382 acceptors
Reading frame   0 time 1.000   Will do grid-seach on 15x15x15 grid,
rcut=0.35
Segmentation fault (core dumped)


The number of donors is correct (I have 86 water molecules) but the number of
acceptors is not.



The number of acceptors is correct.  Water oxygens can be acceptors, so 1296 + 
86 = 1382.



Please, can someone tell me what I am doing wrong?


What GROMACS version are you using?

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] g_hbond problems

2017-03-10 Thread andrea . correa




I am trying to analyze the hydrogen bonds of my simulations by g_hbond.
I am using an index file where  I created two groups: one with  
acceptor atoms (carboxylic oxygen atoms in my structure) and another  
group with the water molecules.


I got a segmentation fault with the message:


Select a group: 6
Selected 6: 'PEI_&_OC'
Select a group: 3
Selected 3: 'Water'
Checking for overlap in atoms between PEI_&_OC and Water
Calculating hydrogen bonds between PEI_&_OC (1296 atoms) and Water  
(258 atoms)

Found 86 donors and 1382 acceptors
Reading frame   0 time 1.000   Will do grid-seach on  
15x15x15 grid, rcut=0.35

Segmentation fault (core dumped)


The number of donors is correct (I have 86 water molecules) but the  
number of acceptors is not.


Please, can someone tell me what I am doing wrong?
Thanks
Andrea

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Re: [gmx-users] g_hbond: range checking error

2016-04-28 Thread Shubhangi Gupta

Hi..

 Thanks for the reply. I was unable to download gromacs-5.1.2; when i
clicked on the link, it showed "the site can't be reached."

However I have been able to figure out the solution. The trajectory file I
was using for analysis of protein-solvent hydrogen bonds did not contain
water coordinates. Now with the trajectory file with both protein and water
coordinates, I have been been to calculate the number of hydrogen bonds
using g_hbond.

Regards,
Shubhangi Gupta
PhD Research Scholar (YUS lab)
Dept of Chemistry
Indian Institute of Technology Bombay
Powai, Mumbai-400076.

Mob: +91 9594229609
e-mail ID: ignahbuhs.gup...@gmail.com
   144033...@iitb.ac.in

On Tue, Apr 26, 2016 at 4:31 PM, Shubhangi Gupta  wrote:

> Hi all,
>
>
>  I want to calculate the number of hydrogen bonds between protein
> and solvent. I am using g_hbond (gromacs 5.0.2) with the two groups -
> protein and SOL. When i run the command, I get a *Range Checking error*
>
> *Variable gx has value -3. It should have been within [0 ..19]*
>
> However when i do the same and choose the two groups as protein and
> protein, the command goes through.
>
> Any help is greatly appreciated.
>
> Thanks
>
>
> Regards,
> Shubhangi Gupta
> PhD Research Scholar (YUS lab)
> Dept of Chemistry
> Indian Institute of Technology Bombay
> Powai, Mumbai-400076.
>
>
> e-mail ID: ignahbuhs.gup...@gmail.com
>144033...@iitb.ac.in
>
>
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Re: [gmx-users] g_hbond: range checking error

2016-04-26 Thread Erik Marklund

Hi,

Strange. Do you get the same error with 5.1.2? If so, can you please file a 
redmine issue (http://redmine.gromacs.org/) and upload the input files that 
generate this error? Assign the issue to me.

Kind regards
Erik Marklund

On 26 Apr 2016, at 12:01, Shubhangi Gupta 
> wrote:

Hi all,


I want to calculate the number of hydrogen bonds between protein
and solvent. I am using g_hbond (gromacs 5.0.2) with the two groups -
protein and SOL. When i run the command, I get a *Range Checking error*

*Variable gx has value -3. It should have been within [0 ..19]*

However when i do the same and choose the two groups as protein and
protein, the command goes through.

Any help is greatly appreciated.

Thanks


Regards,
Shubhangi Gupta
PhD Research Scholar (YUS lab)
Dept of Chemistry
Indian Institute of Technology Bombay
Powai, Mumbai-400076.


e-mail ID: ignahbuhs.gup...@gmail.com
  144033...@iitb.ac.in
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[gmx-users] g_hbond: range checking error

2016-04-26 Thread Shubhangi Gupta

Hi all,


 I want to calculate the number of hydrogen bonds between protein
and solvent. I am using g_hbond (gromacs 5.0.2) with the two groups -
protein and SOL. When i run the command, I get a *Range Checking error*

*Variable gx has value -3. It should have been within [0 ..19]*

However when i do the same and choose the two groups as protein and
protein, the command goes through.

Any help is greatly appreciated.

Thanks


Regards,
Shubhangi Gupta
PhD Research Scholar (YUS lab)
Dept of Chemistry
Indian Institute of Technology Bombay
Powai, Mumbai-400076.


e-mail ID: ignahbuhs.gup...@gmail.com
   144033...@iitb.ac.in
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[gmx-users] g_hbond

2015-09-11 Thread Shahid Nayeem

Dear all
I have used g_hbond with -hbn -hbm flag to get .ndx file and .xpm file.
Then with xpm2ps I converted .xpm to .eps file. I get half the number of
rows in .eps file as compared to .ndx file. when using Justins perl script
I got summary of existence file and here 12 bonds are shown but in .eps
file only 6 rows are plotted. I know that the bonds are plotted in reverse
order but here only half number of bonds are plotted in .eps file. please
help to resolve this issue.
shahid
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Re: [gmx-users] g_hbond

2015-09-11 Thread Justin Lemkul




On 9/11/15 2:43 AM, Shahid Nayeem wrote:

Dear all
I have used g_hbond with -hbn -hbm flag to get .ndx file and .xpm file.
Then with xpm2ps I converted .xpm to .eps file. I get half the number of
rows in .eps file as compared to .ndx file. when using Justins perl script
I got summary of existence file and here 12 bonds are shown but in .eps
file only 6 rows are plotted. I know that the bonds are plotted in reverse
order but here only half number of bonds are plotted in .eps file. please
help to resolve this issue.


You're probably looking at the wrong entry in the index file.  Hard to imagine 
these could be mismatched.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] g_hbond

2015-09-09 Thread Shahid Nayeem

Dear all
I have used g_hbond with -hbn -hbm flag to get .ndx file and .xpm file.
Then with xpm2ps I converted .xpm to .eps file. I get half the number of
rows in .eps file as compared to .ndx file. when using Justins perl script
I got summary of existence file and here 12 bonds are shown but in .eps
file only 6 rows are plotted. I know that the bonds are plotted in reverse
order but here only half number of bonds are plotted in .eps file. please
help to resolve this issue.

shahid
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[gmx-users] g_hbond

2015-08-04 Thread jwillcox

Hello,

I'm trying to use g_hbond to calculate H-bonds between two different
species, but it seems to be counting the donor atom as an acceptor as
well.

e.g. instead of measuring the H-bonds of water to acetate oxygens, it
seems to be measuring the H-bonds of water to acetate oxygens and water
oxygens

Is there a way to specify that I only want to look at the water-acetate
H-bonds and not water-water H-bonds?

Thank you!

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Re: [gmx-users] g_hbond

2015-08-04 Thread Justin Lemkul




On 8/4/15 9:40 AM, jwill...@andrew.cmu.edu wrote:

Hello,

I'm trying to use g_hbond to calculate H-bonds between two different
species, but it seems to be counting the donor atom as an acceptor as
well.

e.g. instead of measuring the H-bonds of water to acetate oxygens, it
seems to be measuring the H-bonds of water to acetate oxygens and water
oxygens

Is there a way to specify that I only want to look at the water-acetate
H-bonds and not water-water H-bonds?



Proper use of index groups will solve this.  You unfortunately haven't provided 
us with any relevant details about how you're doing the calculation, so no one 
can really comment further.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] g_hbond : normalization autocorrelation function.

2015-07-20 Thread Justin Lemkul




On 7/19/15 10:55 AM, Nilesh Dhumal wrote:

Erik,

I want autocorrelation function without normalization.



Use the -nonormalize option.

-Justin


Exact value at t=0, t=1 is with normalization.

Nilesh



Hi Nilesh,

Iâ€™m not sure what you mean. Both Ac_finSys and Ac are 1 at t=0. What
normalisation do you expect?

Kind regards,
Erik

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical  Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ


On 19 Jul 2015, at 04:07, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:

Hello,

I am calculating autocorrelation function without normalization using
g_hbond

g_hbond -f test.pdb -s 3.tpr -nonormalize -n hydrogen_1.ndx -ac
./test/hbac_3.xvg -num ./test/num_3.xvg

The output,  hbac_3.xvg, don't have normalized auto correlation
function.
Here is initial part

@title Hydrogen Bond Autocorrelation
@xaxis  label Time (ps)
@yaxis  label C(t)
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend Ac\sfin sys\v{}\z{}(t)
@ s1 legend Ac(t)
@ s2 legend Cc\scontact,hb\v{}\z{}(t)
@ s3 legend -dAc\sfs\v{}\z{}/dt
 0   1   1  6.67572e-060.761129
  0.050.9619280.99214633980.401535
   0.10.9598460.9917173496   0.0419408
  0.150.9577340.9912813599   0.0340092
   0.20.9564460.99101536600.022918


Why is it not normalized ?

Thanks,

Nilesh

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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] g_hbond : normalization autocorrelation function.

2015-07-19 Thread Nilesh Dhumal

Erik,

I want autocorrelation function without normalization.

Exact value at t=0, t=1 is with normalization.

Nilesh


 Hi Nilesh,

 Iâm not sure what you mean. Both Ac_finSys and Ac are 1 at t=0. What
 normalisation do you expect?

 Kind regards,
 Erik

 Erik Marklund, PhD
 Postdoctoral Research Fellow
 Fulford JRF, Somerville College

 Department of Chemistry
 Physical  Theoretical Chemistry Laboratory
 University of Oxford
 South Parks Road
 Oxford
 OX1 3QZ

 On 19 Jul 2015, at 04:07, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:

 Hello,

 I am calculating autocorrelation function without normalization using
 g_hbond

 g_hbond -f test.pdb -s 3.tpr -nonormalize -n hydrogen_1.ndx -ac
 ./test/hbac_3.xvg -num ./test/num_3.xvg

 The output,  hbac_3.xvg, don't have normalized auto correlation
 function.
 Here is initial part

 @title Hydrogen Bond Autocorrelation
 @xaxis  label Time (ps)
 @yaxis  label C(t)
 @TYPE xy
 @ view 0.15, 0.15, 0.75, 0.85
 @ legend on
 @ legend box on
 @ legend loctype view
 @ legend 0.78, 0.8
 @ legend length 2
 @ s0 legend Ac\sfin sys\v{}\z{}(t)
 @ s1 legend Ac(t)
 @ s2 legend Cc\scontact,hb\v{}\z{}(t)
 @ s3 legend -dAc\sfs\v{}\z{}/dt
 0   1   1  6.67572e-060.761129
  0.050.9619280.99214633980.401535
   0.10.9598460.9917173496   0.0419408
  0.150.9577340.9912813599   0.0340092
   0.20.9564460.99101536600.022918


 Why is it not normalized ?

 Thanks,

 Nilesh

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Re: [gmx-users] g_hbond : normalization autocorrelation function.

2015-07-19 Thread Erik Marklund

Hi Nilesh,

I’m not sure what you mean. Both Ac_finSys and Ac are 1 at t=0. What 
normalisation do you expect?

Kind regards,
Erik

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical  Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

 On 19 Jul 2015, at 04:07, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
 
 Hello,
 
 I am calculating autocorrelation function without normalization using g_hbond
 
 g_hbond -f test.pdb -s 3.tpr -nonormalize -n hydrogen_1.ndx -ac
 ./test/hbac_3.xvg -num ./test/num_3.xvg
 
 The output,  hbac_3.xvg, don't have normalized auto correlation function.
 Here is initial part
 
 @title Hydrogen Bond Autocorrelation
 @xaxis  label Time (ps)
 @yaxis  label C(t)
 @TYPE xy
 @ view 0.15, 0.15, 0.75, 0.85
 @ legend on
 @ legend box on
 @ legend loctype view
 @ legend 0.78, 0.8
 @ legend length 2
 @ s0 legend Ac\sfin sys\v{}\z{}(t)
 @ s1 legend Ac(t)
 @ s2 legend Cc\scontact,hb\v{}\z{}(t)
 @ s3 legend -dAc\sfs\v{}\z{}/dt
 0   1   1  6.67572e-060.761129
  0.050.9619280.99214633980.401535
   0.10.9598460.9917173496   0.0419408
  0.150.9577340.9912813599   0.0340092
   0.20.9564460.99101536600.022918
 
 
 Why is it not normalized ?
 
 Thanks,
 
 Nilesh
 
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[gmx-users] g_hbond : normalization autocorrelation function.

2015-07-18 Thread Nilesh Dhumal

Hello,

I am calculating autocorrelation function without normalization using g_hbond

g_hbond -f test.pdb -s 3.tpr -nonormalize -n hydrogen_1.ndx -ac
./test/hbac_3.xvg -num ./test/num_3.xvg

The output,  hbac_3.xvg, don't have normalized auto correlation function.
Here is initial part

@title Hydrogen Bond Autocorrelation
@xaxis  label Time (ps)
@yaxis  label C(t)
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend Ac\sfin sys\v{}\z{}(t)
@ s1 legend Ac(t)
@ s2 legend Cc\scontact,hb\v{}\z{}(t)
@ s3 legend -dAc\sfs\v{}\z{}/dt
 0   1   1  6.67572e-060.761129
  0.050.9619280.99214633980.401535
   0.10.9598460.9917173496   0.0419408
  0.150.9577340.9912813599   0.0340092
   0.20.9564460.99101536600.022918


Why is it not normalized ?

Thanks,

Nilesh

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Re: [gmx-users] g_hbond

2015-07-11 Thread Erik Marklund

Hi Nilesh,

You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the 
contacts in the last column of hb.xvg.

Kind regards,
Erik

 On 10 Jul 2015, at 15:58, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
 
 I don't understand why am I not getting hydrogen bond,if I use cufoff 0.25nm?
 
 Nilesh
 
 But without contact you will need a full donor-hydrogen-acceptor triad for
 it to be registered, which is not what you want as far as I can tell.
 
 Erik
 
 On 10 Jul 2015, at 15:17, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
 
 This is index file
 
 [ O8-H18-1 ]
  8  18
 [ O8-H18-2 ]
 4032
 
 
 Found 1 donors and 2 acceptors
 
 Its look contact YES check the distance between accetpr---donor.
 
 I will run without contact.
 
 Nilesh
 
 Hi Nilesh,
 
 Am not sure it accepts hydrogens as donors/acceptors even with
 -contact.
 How many donors and acceptors are found?
 
 Kind regards,
 Erik
 
 On 10 Jul 2015, at 14:37, Nilesh Dhumal ndhu...@andrew.cmu.edu
 wrote:
 
 I calculated number of hydrogen bond with cutoff 0.25 nm (Distance
 between
 hydrogen and O,acceptor) using g_hbond,
 
 g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg
 -nonitacc
 -r 0.25 -contact -dist
 
 The found the calculated number of hydrogen bond along time are zero
 and
 -nan is the in hbdist.xvg file.
 I calculated the distance between hydrogen and oxygen using g_dist and
 the
 calculated the distance is less than 0.25 nm.
 
 Why am I getting zero number of hydrogen bonds using g_hbond (based on
 same cutoff )?
 
 Nilesh
 
 
 
 Thanks.
 
 I will use two groups.
 
 Nilesh
 
 On 7/9/15 9:13 PM, Nilesh Dhumal wrote:
 
 
 On 7/9/15 9:02 PM, Nilesh Dhumal wrote:
 Hello,
 
 I am calculating g_hbond for water system.  I have a question
 about
 specifying two group for calculating hydrogen bond.
 
 Do I specify atoms in triplet(O-H---O)?
 Can I specify O-H as one group (Donor-Hydrogen) and O in other
 group
 (Acceptor)?
 
 If the system is pure water, you do not need any special index
 groups.
 
 I have DMSO in the system. I just mentioned water to make it
 simple.
 I am interested in O--H---O(DMSO) interactions?
 
 How should I specify this?
 
 With one triplet O--H---O(DMSO) or two groups one O--H and second
 O(DMSO)
 
 The latter - just use DMSO and water groups.  O can be a donor or
 acceptor, and
 g_hbond intelligently figures out whether or not a given atom is a
 donor
 or
 acceptor (or both).
 
 -Justin
 
 
 Default  -r cutoff is 0.35nm. Is the distance between
 hydrogen---acceptor
 or distance between donor---acceptor?
 
 Read the first sentence of the help description.
 
 -Justin
 
 --
 ==
 
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
 
 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
 
 ==
 --
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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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 send
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 --
 ==
 
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
 
 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
 
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Re: [gmx-users] g_hbond

2015-07-11 Thread Nilesh Dhumal

Hello Erik,

I did the same.

Thanks,

Nilesh

 Hi Nilesh,

 You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the
 contacts in the last column of hb.xvg.

 Kind regards,
 Erik

 On 10 Jul 2015, at 15:58, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:

 I don't understand why am I not getting hydrogen bond,if I use cufoff
 0.25nm?

 Nilesh

 But without contact you will need a full donor-hydrogen-acceptor triad
 for
 it to be registered, which is not what you want as far as I can tell.

 Erik

 On 10 Jul 2015, at 15:17, Nilesh Dhumal ndhu...@andrew.cmu.edu
 wrote:

 This is index file

 [ O8-H18-1 ]
  8  18
 [ O8-H18-2 ]
 4032


 Found 1 donors and 2 acceptors

 Its look contact YES check the distance between accetpr---donor.

 I will run without contact.

 Nilesh

 Hi Nilesh,

 Am not sure it accepts hydrogens as donors/acceptors even with
 -contact.
 How many donors and acceptors are found?

 Kind regards,
 Erik

 On 10 Jul 2015, at 14:37, Nilesh Dhumal ndhu...@andrew.cmu.edu
 wrote:

 I calculated number of hydrogen bond with cutoff 0.25 nm (Distance
 between
 hydrogen and O,acceptor) using g_hbond,

 g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg
 -nonitacc
 -r 0.25 -contact -dist

 The found the calculated number of hydrogen bond along time are zero
 and
 -nan is the in hbdist.xvg file.
 I calculated the distance between hydrogen and oxygen using g_dist
 and
 the
 calculated the distance is less than 0.25 nm.

 Why am I getting zero number of hydrogen bonds using g_hbond (based
 on
 same cutoff )?

 Nilesh



 Thanks.

 I will use two groups.

 Nilesh

 On 7/9/15 9:13 PM, Nilesh Dhumal wrote:


 On 7/9/15 9:02 PM, Nilesh Dhumal wrote:
 Hello,

 I am calculating g_hbond for water system.  I have a question
 about
 specifying two group for calculating hydrogen bond.

 Do I specify atoms in triplet(O-H---O)?
 Can I specify O-H as one group (Donor-Hydrogen) and O in other
 group
 (Acceptor)?

 If the system is pure water, you do not need any special index
 groups.

 I have DMSO in the system. I just mentioned water to make it
 simple.
 I am interested in O--H---O(DMSO) interactions?

 How should I specify this?

 With one triplet O--H---O(DMSO) or two groups one O--H and second
 O(DMSO)

 The latter - just use DMSO and water groups.  O can be a donor or
 acceptor, and
 g_hbond intelligently figures out whether or not a given atom is a
 donor
 or
 acceptor (or both).

 -Justin


 Default  -r cutoff is 0.35nm. Is the distance between
 hydrogen---acceptor
 or distance between donor---acceptor?

 Read the first sentence of the help description.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
 before
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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
 or
 send
 a mail to gmx-users-requ...@gromacs.org.




 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
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Re: [gmx-users] g_hbond

2015-07-10 Thread Nilesh Dhumal

I don't understand why am I not getting hydrogen bond,if I use cufoff 0.25nm?

Nilesh

 But without contact you will need a full donor-hydrogen-acceptor triad for
 it to be registered, which is not what you want as far as I can tell.

 Erik

 On 10 Jul 2015, at 15:17, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:

 This is index file

 [ O8-H18-1 ]
   8  18
 [ O8-H18-2 ]
 4032


 Found 1 donors and 2 acceptors

 Its look contact YES check the distance between accetpr---donor.

 I will run without contact.

 Nilesh

 Hi Nilesh,

 Am not sure it accepts hydrogens as donors/acceptors even with
 -contact.
 How many donors and acceptors are found?

 Kind regards,
 Erik

 On 10 Jul 2015, at 14:37, Nilesh Dhumal ndhu...@andrew.cmu.edu
 wrote:

 I calculated number of hydrogen bond with cutoff 0.25 nm (Distance
 between
 hydrogen and O,acceptor) using g_hbond,

 g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg
 -nonitacc
 -r 0.25 -contact -dist

 The found the calculated number of hydrogen bond along time are zero
 and
 -nan is the in hbdist.xvg file.
 I calculated the distance between hydrogen and oxygen using g_dist and
 the
 calculated the distance is less than 0.25 nm.

 Why am I getting zero number of hydrogen bonds using g_hbond (based on
 same cutoff )?

 Nilesh



 Thanks.

 I will use two groups.

 Nilesh

 On 7/9/15 9:13 PM, Nilesh Dhumal wrote:


 On 7/9/15 9:02 PM, Nilesh Dhumal wrote:
 Hello,

 I am calculating g_hbond for water system.  I have a question
 about
 specifying two group for calculating hydrogen bond.

 Do I specify atoms in triplet(O-H---O)?
 Can I specify O-H as one group (Donor-Hydrogen) and O in other
 group
 (Acceptor)?

 If the system is pure water, you do not need any special index
 groups.

 I have DMSO in the system. I just mentioned water to make it
 simple.
 I am interested in O--H---O(DMSO) interactions?

 How should I specify this?

 With one triplet O--H---O(DMSO) or two groups one O--H and second
 O(DMSO)

 The latter - just use DMSO and water groups.  O can be a donor or
 acceptor, and
 g_hbond intelligently figures out whether or not a given atom is a
 donor
 or
 acceptor (or both).

 -Justin


 Default  -r cutoff is 0.35nm. Is the distance between
 hydrogen---acceptor
 or distance between donor---acceptor?

 Read the first sentence of the help description.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
 or
 send
 a mail to gmx-users-requ...@gromacs.org.




 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
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Re: [gmx-users] g_hbond

2015-07-10 Thread Erik Marklund

But without contact you will need a full donor-hydrogen-acceptor triad for it 
to be registered, which is not what you want as far as I can tell.

Erik

 On 10 Jul 2015, at 15:17, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
 
 This is index file
 
 [ O8-H18-1 ]
   8  18
 [ O8-H18-2 ]
 4032
 
 
 Found 1 donors and 2 acceptors
 
 Its look contact YES check the distance between accetpr---donor.
 
 I will run without contact.
 
 Nilesh
 
 Hi Nilesh,
 
 Am not sure it accepts hydrogens as donors/acceptors even with -contact.
 How many donors and acceptors are found?
 
 Kind regards,
 Erik
 
 On 10 Jul 2015, at 14:37, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
 
 I calculated number of hydrogen bond with cutoff 0.25 nm (Distance
 between
 hydrogen and O,acceptor) using g_hbond,
 
 g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg
 -nonitacc
 -r 0.25 -contact -dist
 
 The found the calculated number of hydrogen bond along time are zero and
 -nan is the in hbdist.xvg file.
 I calculated the distance between hydrogen and oxygen using g_dist and
 the
 calculated the distance is less than 0.25 nm.
 
 Why am I getting zero number of hydrogen bonds using g_hbond (based on
 same cutoff )?
 
 Nilesh
 
 
 
 Thanks.
 
 I will use two groups.
 
 Nilesh
 
 On 7/9/15 9:13 PM, Nilesh Dhumal wrote:
 
 
 On 7/9/15 9:02 PM, Nilesh Dhumal wrote:
 Hello,
 
 I am calculating g_hbond for water system.  I have a question about
 specifying two group for calculating hydrogen bond.
 
 Do I specify atoms in triplet(O-H---O)?
 Can I specify O-H as one group (Donor-Hydrogen) and O in other
 group
 (Acceptor)?
 
 If the system is pure water, you do not need any special index
 groups.
 
 I have DMSO in the system. I just mentioned water to make it simple.
 I am interested in O--H---O(DMSO) interactions?
 
 How should I specify this?
 
 With one triplet O--H---O(DMSO) or two groups one O--H and second
 O(DMSO)
 
 The latter - just use DMSO and water groups.  O can be a donor or
 acceptor, and
 g_hbond intelligently figures out whether or not a given atom is a
 donor
 or
 acceptor (or both).
 
 -Justin
 
 
 Default  -r cutoff is 0.35nm. Is the distance between
 hydrogen---acceptor
 or distance between donor---acceptor?
 
 Read the first sentence of the help description.
 
 -Justin
 
 --
 ==
 
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
 
 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
 
 ==
 --
 Gromacs Users mailing list
 
 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
 or
 send
 a mail to gmx-users-requ...@gromacs.org.
 
 
 
 
 --
 ==
 
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
 
 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
 
 ==
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Re: [gmx-users] g_hbond

2015-07-10 Thread Nilesh Dhumal

I calculated number of hydrogen bond with cutoff 0.25 nm (Distance between
hydrogen and O,acceptor) using g_hbond,

g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg -nonitacc
-r 0.25 -contact -dist

The found the calculated number of hydrogen bond along time are zero and
-nan is the in hbdist.xvg file.
I calculated the distance between hydrogen and oxygen using g_dist and the
calculated the distance is less than 0.25 nm.

Why am I getting zero number of hydrogen bonds using g_hbond (based on
same cutoff )?

Nilesh



 Thanks.

 I will use two groups.

 Nilesh

 On 7/9/15 9:13 PM, Nilesh Dhumal wrote:


 On 7/9/15 9:02 PM, Nilesh Dhumal wrote:
 Hello,

 I am calculating g_hbond for water system.  I have a question about
 specifying two group for calculating hydrogen bond.

 Do I specify atoms in triplet(O-H---O)?
 Can I specify O-H as one group (Donor-Hydrogen) and O in other group
 (Acceptor)?

 If the system is pure water, you do not need any special index groups.

 I have DMSO in the system. I just mentioned water to make it simple.
 I am interested in O--H---O(DMSO) interactions?

 How should I specify this?

 With one triplet O--H---O(DMSO) or two groups one O--H and second
 O(DMSO)

 The latter - just use DMSO and water groups.  O can be a donor or
 acceptor, and
 g_hbond intelligently figures out whether or not a given atom is a donor
 or
 acceptor (or both).

 -Justin


 Default  -r cutoff is 0.35nm. Is the distance between
 hydrogen---acceptor
 or distance between donor---acceptor?

 Read the first sentence of the help description.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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 * 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.




 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
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Re: [gmx-users] g_hbond

2015-07-10 Thread Nilesh Dhumal

This is index file

[ O8-H18-1 ]
   8  18
[ O8-H18-2 ]
4032


Found 1 donors and 2 acceptors

Its look contact YES check the distance between accetpr---donor.

I will run without contact.

Nilesh

 Hi Nilesh,

 Am not sure it accepts hydrogens as donors/acceptors even with -contact.
 How many donors and acceptors are found?

 Kind regards,
 Erik

 On 10 Jul 2015, at 14:37, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:

 I calculated number of hydrogen bond with cutoff 0.25 nm (Distance
 between
 hydrogen and O,acceptor) using g_hbond,

 g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg
 -nonitacc
 -r 0.25 -contact -dist

 The found the calculated number of hydrogen bond along time are zero and
 -nan is the in hbdist.xvg file.
 I calculated the distance between hydrogen and oxygen using g_dist and
 the
 calculated the distance is less than 0.25 nm.

 Why am I getting zero number of hydrogen bonds using g_hbond (based on
 same cutoff )?

 Nilesh



 Thanks.

 I will use two groups.

 Nilesh

 On 7/9/15 9:13 PM, Nilesh Dhumal wrote:


 On 7/9/15 9:02 PM, Nilesh Dhumal wrote:
 Hello,

 I am calculating g_hbond for water system.  I have a question about
 specifying two group for calculating hydrogen bond.

 Do I specify atoms in triplet(O-H---O)?
 Can I specify O-H as one group (Donor-Hydrogen) and O in other
 group
 (Acceptor)?

 If the system is pure water, you do not need any special index
 groups.

 I have DMSO in the system. I just mentioned water to make it simple.
 I am interested in O--H---O(DMSO) interactions?

 How should I specify this?

 With one triplet O--H---O(DMSO) or two groups one O--H and second
 O(DMSO)

 The latter - just use DMSO and water groups.  O can be a donor or
 acceptor, and
 g_hbond intelligently figures out whether or not a given atom is a
 donor
 or
 acceptor (or both).

 -Justin


 Default  -r cutoff is 0.35nm. Is the distance between
 hydrogen---acceptor
 or distance between donor---acceptor?

 Read the first sentence of the help description.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
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 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] g_hbond

2015-07-10 Thread Erik Marklund

Hi Nilesh,

Am not sure it accepts hydrogens as donors/acceptors even with -contact. How 
many donors and acceptors are found?

Kind regards,
Erik

 On 10 Jul 2015, at 14:37, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
 
 I calculated number of hydrogen bond with cutoff 0.25 nm (Distance between
 hydrogen and O,acceptor) using g_hbond,
 
 g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg -nonitacc
 -r 0.25 -contact -dist
 
 The found the calculated number of hydrogen bond along time are zero and
 -nan is the in hbdist.xvg file.
 I calculated the distance between hydrogen and oxygen using g_dist and the
 calculated the distance is less than 0.25 nm.
 
 Why am I getting zero number of hydrogen bonds using g_hbond (based on
 same cutoff )?
 
 Nilesh
 
 
 
 Thanks.
 
 I will use two groups.
 
 Nilesh
 
 On 7/9/15 9:13 PM, Nilesh Dhumal wrote:
 
 
 On 7/9/15 9:02 PM, Nilesh Dhumal wrote:
 Hello,
 
 I am calculating g_hbond for water system.  I have a question about
 specifying two group for calculating hydrogen bond.
 
 Do I specify atoms in triplet(O-H---O)?
 Can I specify O-H as one group (Donor-Hydrogen) and O in other group
 (Acceptor)?
 
 If the system is pure water, you do not need any special index groups.
 
 I have DMSO in the system. I just mentioned water to make it simple.
 I am interested in O--H---O(DMSO) interactions?
 
 How should I specify this?
 
 With one triplet O--H---O(DMSO) or two groups one O--H and second
 O(DMSO)
 
 The latter - just use DMSO and water groups.  O can be a donor or
 acceptor, and
 g_hbond intelligently figures out whether or not a given atom is a donor
 or
 acceptor (or both).
 
 -Justin
 
 
 Default  -r cutoff is 0.35nm. Is the distance between
 hydrogen---acceptor
 or distance between donor---acceptor?
 
 Read the first sentence of the help description.
 
 -Justin
 
 --
 ==
 
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
 
 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
 
 ==
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 --
 ==
 
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
 
 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
 
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[gmx-users] g_hbond

2015-07-09 Thread Nilesh Dhumal

Hello,

I am calculating g_hbond for water system.  I have a question about
specifying two group for calculating hydrogen bond.

Do I specify atoms in triplet(O-H---O)?
Can I specify O-H as one group (Donor-Hydrogen) and O in other group
(Acceptor)?
Default  -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor
or distance between donor---acceptor?

Thanks,

Nilesh

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Re: [gmx-users] g_hbond

2015-07-09 Thread Nilesh Dhumal

Thanks.

I will use two groups.

Nilesh

 On 7/9/15 9:13 PM, Nilesh Dhumal wrote:


 On 7/9/15 9:02 PM, Nilesh Dhumal wrote:
 Hello,

 I am calculating g_hbond for water system.  I have a question about
 specifying two group for calculating hydrogen bond.

 Do I specify atoms in triplet(O-H---O)?
 Can I specify O-H as one group (Donor-Hydrogen) and O in other group
 (Acceptor)?

 If the system is pure water, you do not need any special index groups.

 I have DMSO in the system. I just mentioned water to make it simple.
 I am interested in O--H---O(DMSO) interactions?

 How should I specify this?

 With one triplet O--H---O(DMSO) or two groups one O--H and second
 O(DMSO)

 The latter - just use DMSO and water groups.  O can be a donor or
 acceptor, and
 g_hbond intelligently figures out whether or not a given atom is a donor
 or
 acceptor (or both).

 -Justin


 Default  -r cutoff is 0.35nm. Is the distance between
 hydrogen---acceptor
 or distance between donor---acceptor?

 Read the first sentence of the help description.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
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 send
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 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
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Re: [gmx-users] g_hbond

2015-07-09 Thread Nilesh Dhumal



 On 7/9/15 9:02 PM, Nilesh Dhumal wrote:
 Hello,

 I am calculating g_hbond for water system.  I have a question about
 specifying two group for calculating hydrogen bond.

 Do I specify atoms in triplet(O-H---O)?
 Can I specify O-H as one group (Donor-Hydrogen) and O in other group
 (Acceptor)?

 If the system is pure water, you do not need any special index groups.

I have DMSO in the system. I just mentioned water to make it simple.
I am interested in O--H---O(DMSO) interactions?

How should I specify this?

With one triplet O--H---O(DMSO) or two groups one O--H and second O(DMSO)

 Default  -r cutoff is 0.35nm. Is the distance between
 hydrogen---acceptor
 or distance between donor---acceptor?

 Read the first sentence of the help description.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
 Gromacs Users mailing list

 * Please search the archive at
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Re: [gmx-users] g_hbond

2015-07-09 Thread Justin Lemkul




On 7/9/15 9:13 PM, Nilesh Dhumal wrote:



On 7/9/15 9:02 PM, Nilesh Dhumal wrote:

Hello,

I am calculating g_hbond for water system.  I have a question about
specifying two group for calculating hydrogen bond.

Do I specify atoms in triplet(O-H---O)?
Can I specify O-H as one group (Donor-Hydrogen) and O in other group
(Acceptor)?


If the system is pure water, you do not need any special index groups.


I have DMSO in the system. I just mentioned water to make it simple.
I am interested in O--H---O(DMSO) interactions?

How should I specify this?

With one triplet O--H---O(DMSO) or two groups one O--H and second O(DMSO)


The latter - just use DMSO and water groups.  O can be a donor or acceptor, and 
g_hbond intelligently figures out whether or not a given atom is a donor or 
acceptor (or both).


-Justin




Default  -r cutoff is 0.35nm. Is the distance between
hydrogen---acceptor
or distance between donor---acceptor?


Read the first sentence of the help description.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] g_hbond

2015-07-09 Thread Justin Lemkul




On 7/9/15 9:02 PM, Nilesh Dhumal wrote:

Hello,

I am calculating g_hbond for water system.  I have a question about
specifying two group for calculating hydrogen bond.

Do I specify atoms in triplet(O-H---O)?
Can I specify O-H as one group (Donor-Hydrogen) and O in other group
(Acceptor)?


If the system is pure water, you do not need any special index groups.


Default  -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor
or distance between donor---acceptor?


Read the first sentence of the help description.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] g_hbond on trajectory

2015-06-02 Thread Jennifer Vo

Dear All,
I used g_hbond to analyze the possible hydrogen bonds between protein and
solvent (water) over the trajectory with this command:
g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg -g
hbond.log -dist hbdist.xvg -nhbdist nhbdist.xvg

The log file showed me:

  SER141OG  SER141HG SOL2920OW
  SER141OG  SER141HG SOL4449OW
  SER141OG  SER141HG SOL5073OW
  SER141OG  SER141HG SOL11886OW
  SER141OG  SER141HG SOL13715OW

I wonder if this calculation is based on one coordinate file (if yes, which
one!?) or the average structure over trajectory?
Many thanks in advance.
Regards,
Jennifer
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Re: [gmx-users] g_hbond on trajectory

2015-06-02 Thread Justin Lemkul




On 6/2/15 5:01 AM, Jennifer Vo wrote:

Dear All,
I used g_hbond to analyze the possible hydrogen bonds between protein and
solvent (water) over the trajectory with this command:
g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg -g
hbond.log -dist hbdist.xvg -nhbdist nhbdist.xvg

The log file showed me:

   SER141OG  SER141HG SOL2920OW
   SER141OG  SER141HG SOL4449OW
   SER141OG  SER141HG SOL5073OW
   SER141OG  SER141HG SOL11886OW
   SER141OG  SER141HG SOL13715OW

I wonder if this calculation is based on one coordinate file (if yes, which
one!?) or the average structure over trajectory?


Trajectory analysis is done for every frame in the trajectory.  The log output 
just indicates that different waters were hydrogen bonded to that particular Ser 
at different times.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] g_hbond on trajectory

2015-06-02 Thread Jennifer Vo

Thank you, Justin.
Jennifer


On Tue, Jun 2, 2015 at 2:09 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/2/15 5:01 AM, Jennifer Vo wrote:

 Dear All,
 I used g_hbond to analyze the possible hydrogen bonds between protein and
 solvent (water) over the trajectory with this command:
 g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg
 -g
 hbond.log -dist hbdist.xvg -nhbdist nhbdist.xvg

 The log file showed me:
 
SER141OG  SER141HG SOL2920OW
SER141OG  SER141HG SOL4449OW
SER141OG  SER141HG SOL5073OW
SER141OG  SER141HG SOL11886OW
SER141OG  SER141HG SOL13715OW
 
 I wonder if this calculation is based on one coordinate file (if yes,
 which
 one!?) or the average structure over trajectory?


 Trajectory analysis is done for every frame in the trajectory.  The log
 output just indicates that different waters were hydrogen bonded to that
 particular Ser at different times.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
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[gmx-users] g_hbond never shows hbond with HW2

2015-05-01 Thread Ebert Maximilian

Dear list,

I discovered something strange today. In my hbond search i find only HW1 of the 
water forming a hydrogen bond as donor hydrogen and never HW2. Is this due to 
the fact that I am using SPC water? I can see the atom IDs of HW2 in the [ 
donors_hydrogens_Water ] entry in the ndx file. So technically GROMACs searched 
for HW2 donor connections but never finds any. However, thousands of hbonds are 
found with HW1.

Any thoughts on that? Thanks,

Max
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Re: [gmx-users] g_hbond never shows hbond with HW2

2015-05-01 Thread Justin Lemkul




On 5/1/15 11:27 AM, Ebert Maximilian wrote:

Dear list,

I discovered something strange today. In my hbond search i find only HW1 of the 
water forming a hydrogen bond as donor hydrogen and never HW2. Is this due to 
the fact that I am using SPC water? I can see the atom IDs of HW2 in the [ 
donors_hydrogens_Water ] entry in the ndx file. So technically GROMACs searched 
for HW2 donor connections but never finds any. However, thousands of hbonds are 
found with HW1.

Any thoughts on that? Thanks,



This is default behavior because of -merge.  If you want to differentiate 
between different H on the same donor, use -nomerge.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] g_hbond not running

2015-01-06 Thread Erik Marklund

Hi,

There’s an issue with g_hbond assuming periodic boundary conditions. I will try
to fix this.

Kind regards,
Erik

On 17 Dec 2014, at 12:05, Erik Marklund erik.markl...@chem.ox.ac.uk wrote:

Hi Toni,

Or better still, you can file a redmine issue and upload the files there:
http://redmine.gromacs.org. It facilitates bugfixing and makes sure it's not
forgotten.

Erik

On 17 Dec 2014, at 09:26, antoni borysik
bory...@hotmail.co.ukmailto:bory...@hotmail.co.uk wrote:

will do thanks a lot.
Toni

From: erik.markl...@chem.ox.ac.ukmailto:erik.markl...@chem.ox.ac.uk
To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org
Date: Wed, 17 Dec 2014 09:15:41 +
Subject: Re: [gmx-users] g_hbond not running

Hi Tony,

Would you mind sending me the tpr and trr off list so I can have a closer
look and maybe debug?

Erik

On 17 Dec 2014, at 09:10, antoni borysik
bory...@hotmail.co.ukmailto:bory...@hotmail.co.uk wrote:

Hi Erik - yes tried that and no luck. g_hbond runs well with with some
simulation but not others. Can't figure it out, or why no-one has come across
this one before.

From: erik.markl...@chem.ox.ac.ukmailto:erik.markl...@chem.ox.ac.uk
To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org
Date: Tue, 16 Dec 2014 14:50:15 +
Subject: Re: [gmx-users] g_hbond not running

Hi Toni,

Have you tried with -nthreads 1, which effectively turns off the parallel
grid search? Never seen/heard of this problem before.

Kind regards,
Erik

Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 16 Dec 2014, at 14:11, antoni borysik
bory...@hotmail.co.ukmailto:bory...@hotmail.co.ukmailto:bory...@hotmail.co.uk
wrote:

Hi, have run various vacuum simulations with GROMACS 4.6.7. I find I can
calculate h-bonds using g_hbond -f md.trr -s md.tpr on some simulations just
fine while on others the system freezes 'Frame loop parallelized with OpenMP
using 32 threads' even after leaving 12 hours there is no progress or
error. I have not found this problem on the web nor been able to sort out
myself - any insight would be most appreciated.

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