Re: [gmx-users] g_dist problem in Implicit solvent

[Justin Lemkul]

On 5/15/13 7:15 PM, Tong Li wrote:

Hi Justin,

I really appreciate your reply! I finally solved the problem: change the 
machine…

I have no idea why this happens, the machine I run simulation on is HP Z600,
Ubuntu. The package is directly installed from the ‘Ubuntu software center’.
This system is installed one month ago, it is Ubuntu 12.10. The simulation runs
perfectly on the machine. However, after the simulation, my post processing got
the aforementioned problem. I checked a whole day but didn’t get any clue,
totally lost myself. When I was about to leave my office yesterday, I did my
last try on the HPC server from our university. It finished, without any 
problem.

I guess it is due to the automatically installation of Gromacs on my HP Z600.
Anyway, the problem is solved, even though I still have no idea why that bug
happened.

Thank you so much for your help and sorry about the annoying question I 
proposed.



It's not annoying.  On the contrary, it's very useful to know that there might 
be broken packages out there in case someone else runs into it.  For what it's 
worth, I have had problems with Ubuntu packages in the past, though my issues 
were related to pdb2gmx.  It is for this reason that, to this day, I always 
install Gromacs myself from source.


-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


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Re: [gmx-users] g_dist problem in Implicit solvent

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 5/14/13 11:37 PM, Tong Li wrote:

Hi Justin,

Really appreciate your prompt reply! I got the inconsistence, the atom index in
the original tpr file is different with the ones in xtc result file. However, I
have no ideas what caused this… Some atoms are not in the ‘tpr’ file, but appear
in the traj file (xtc) and also in the output geometry file (gro).



This is impossible.  If atoms are not in a .tpr file, they can't be written to 
configurations and trajectories.  Have you mixed up any of your files?  Use of 
gmxcheck and gmxdump will clarify what you have in what file.


-Justin


I was using absolute implicit solvent simulation, never used any or deduct any
water molecules from the simulation system. From geometry optimization, to nvt
relaxation, then steered MD simulation in nvt assemble.

Thanks a lot for your kind help!

Cheers,

Tong

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype  = cut-off

rcoulomb = 1.2

; Relative dielectric constant for the medium and the reaction field

epsilon_r= 2

epsilon_rf   = 0

; Method for doing Van der Waals

vdw-type = cut-off

; cut-off lengths

rvdw = 1.2

; Temperature coupling is on

tcoupl   = Berendsen  ; modified Berendsen thermostat

tc-grps  = Protein Non-Protein   ; two coupling groups - more
accurate

tau_t = 0.1  0.1  ; time constant, in ps

ref_t  = 310 310 ; reference temperature, one
for each group, in K

implicit-solvent = GBSA

algorithm  = HCT

rgbradii  = 1.2

; pull code

pull= umbrella

pull_geometry   = distance

pull_dim= Y Y Y

pull_start  = yes

pull_ngroups= 1

pull_group0 = non-Protein

pull_group1 = Protein

pull_init1  = 0

pull_rate1  = -2

pull_k1 = 2000  ; kJ mol^-1 nm^-2

pull_nstxout= 100  ; every 0.2 ps

pull_nstfout= 100  ; every 0.2 ps



--


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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Re: [gmx-users] g_dist problem in Implicit solvent

[Justin Lemkul]

On 5/14/13 7:26 PM, Tong Li wrote:

Dear All,

I got this problem recently. I want to use g_dist to calculate the distance 
between two group in my simulation system. However, when I use the implicit 
solvent for simulation, g_dist went into this problem: Molecule in topology has 
atom numbers below and above natoms.

I have used tpbconv to create a new tpr file, and also used gmxcheck to check 
my traj file, they are all consistent. Also, I have never run into this problem 
when I was using explicit solvent. Hence, I highly suspect this problem comes 
from the implicit solvent.



So, just to clarify, did you run an implicit solvent simulation, or did you 
simply remove the water from your .tpr file to do analysis and post-processing? 
 The latter is particularly error-prone and can be the source of your problem. 
 I have never had issues in using analysis tools with true implicit solvent 
simulations.


In any case, gmxcheck should be useful in telling you about the contents of the 
index groups.  Just because there are the "right" number of atoms in the system, 
does not mean that the atom numbers are necessarily within that number if you 
stripped other coordinates out.


-Justin


Really appreciate that you can help me go through this. Thanks a lot!

Cheers,
Tony

 :-)  g_dist  (-:

Option Filename  Type Description

   -f   traj.trr  InputTrajectory: xtc trr trj gro g96 pdb cpt
   -snowater.tpr  InputRun input file: tpr tpb tpa
   -n  index.ndx  Input, Opt!  Index file
   -o   dist.xvg  Output, Opt. xvgr/xmgr file
-lt   lifetime.xvg  Output, Opt. xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint19  Set the nicelevel
-b   time   0   First frame (ps) to read from trajectory
-e   time   0   Last frame (ps) to read from trajectory
-dt  time   0   Only use frame when t MOD dt = first time (ps)
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-distreal   0   Print all atoms in group 2 closer than dist to
 the center of mass of group 1

Reading file nowater.tpr, VERSION 4.5.5 (single precision)
Group 0 ( System) has 10199 elements
Group 1 (  Other) has  4372 elements
Group 2 (GRA) has  3936 elements
Group 3 (ORA) has   223 elements
Group 4 (HRA) has   213 elements
Group 5 (Protein) has  5827 elements
Group 6 (  Protein-H) has  2933 elements
Group 7 (C-alpha) has   375 elements
Group 8 (   Backbone) has  1125 elements
Group 9 (  MainChain) has  1501 elements
Group10 (   MainChain+Cb) has  1848 elements
Group11 (MainChain+H) has  1859 elements
Group12 (  SideChain) has  3968 elements
Group13 (SideChain-H) has  1432 elements
Group14 (Prot-Masses) has  5827 elements
Group15 (non-Protein) has  4372 elements
Select a group: 1
Selected 1: 'Other'
Select a group: 14
Selected 14: 'Prot-Masses'
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
Back Off! I just backed up dist.xvg to ./#dist.xvg.1#

---
Program g_dist, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/mshift.c, line: 102

Fatal error:
Molecule in topology has atom numbers below and above natoms (10198).
You are probably trying to use a trajectory which does not match the first 
10198 atoms of the run input file.
You can make a matching run input file with tpbconv.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"There's No Room For the Weak" (Joy Division)



--


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_dist problem in Implicit solvent

[Tong Li]

Dear All,

I got this problem recently. I want to use g_dist to calculate the distance 
between two group in my simulation system. However, when I use the implicit 
solvent for simulation, g_dist went into this problem: Molecule in topology has 
atom numbers below and above natoms.

I have used tpbconv to create a new tpr file, and also used gmxcheck to check 
my traj file, they are all consistent. Also, I have never run into this problem 
when I was using explicit solvent. Hence, I highly suspect this problem comes 
from the implicit solvent.

Really appreciate that you can help me go through this. Thanks a lot!

Cheers,
Tony

:-)  g_dist  (-:

Option Filename  Type Description

  -f   traj.trr  InputTrajectory: xtc trr trj gro g96 pdb cpt
  -snowater.tpr  InputRun input file: tpr tpb tpa
  -n  index.ndx  Input, Opt!  Index file
  -o   dist.xvg  Output, Opt. xvgr/xmgr file
-lt   lifetime.xvg  Output, Opt. xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint19  Set the nicelevel
-b   time   0   First frame (ps) to read from trajectory
-e   time   0   Last frame (ps) to read from trajectory
-dt  time   0   Only use frame when t MOD dt = first time (ps)
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-distreal   0   Print all atoms in group 2 closer than dist to
the center of mass of group 1

Reading file nowater.tpr, VERSION 4.5.5 (single precision)
Group 0 ( System) has 10199 elements
Group 1 (  Other) has  4372 elements
Group 2 (GRA) has  3936 elements
Group 3 (ORA) has   223 elements
Group 4 (HRA) has   213 elements
Group 5 (Protein) has  5827 elements
Group 6 (  Protein-H) has  2933 elements
Group 7 (C-alpha) has   375 elements
Group 8 (   Backbone) has  1125 elements
Group 9 (  MainChain) has  1501 elements
Group10 (   MainChain+Cb) has  1848 elements
Group11 (MainChain+H) has  1859 elements
Group12 (  SideChain) has  3968 elements
Group13 (SideChain-H) has  1432 elements
Group14 (Prot-Masses) has  5827 elements
Group15 (non-Protein) has  4372 elements
Select a group: 1
Selected 1: 'Other'
Select a group: 14
Selected 14: 'Prot-Masses'
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
Back Off! I just backed up dist.xvg to ./#dist.xvg.1#

---
Program g_dist, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/mshift.c, line: 102

Fatal error:
Molecule in topology has atom numbers below and above natoms (10198).
You are probably trying to use a trajectory which does not match the first 
10198 atoms of the run input file.
You can make a matching run input file with tpbconv.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"There's No Room For the Weak" (Joy Division)

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Re: [gmx-users] g_dist

[Justin Lemkul]

On 5/12/13 8:48 AM, mohammad agha wrote:

Dear GROMACS Specialists,

I want to obtain number of instances the different atoms was found within a 
spherical shell of width 0.02 nm at a distance r
from the micelle COM. For this, I use g_dist -dist, but when I select for 
example 0.04, it also result all instances in 0-0.02, whereas I want only 
instances in 0.02-0.04. May I ask you to help me, Please?



What you need is a histogram, with a bin width of 0.02 nm.  g_dist won't do this 
for you.  g_analyze -dist -bw 0.02 will do that based on whatever input data you 
give it, though the direct output of g_dist -dist probably isn't in the right 
format.


-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


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[gmx-users] g_dist

[mohammad agha]

Dear GROMACS Specialists,

I want to obtain number of instances the different atoms was found within a 
spherical shell of width 0.02 nm at a distance r
from the micelle COM. For this, I use g_dist -dist, but when I select for 
example 0.04, it also result all instances in 0-0.02, whereas I want only 
instances in 0.02-0.04. May I ask you to help me, Please?

Best Regards
Sara   
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Re: [gmx-users] g_dist

[Justin Lemkul]

On 5/10/13 11:46 AM, mohammad agha wrote:

Dear Justin,


Thank you very much from your answer.
May I ask you to help me more, Please?
I work with UBUNTU, I don't know how should I do it!



Apply Google.  This is not a Gromacs issue and should be investigated and 
studied in the appropriate forum.


-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


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[gmx-users] g_dist

[mohammad agha]

Dear Justin,

Thank you very much from your help.

Best Regards
Sara

On 5/10/13 11:27 AM, mohammad agha wrote:
> Dear GROMACS Specialists,
> I have one problem with g_dist. When I use g_dist along with option -dist, 
> the output is printed on the terminal, but I want them into a file as 
> separately.
> May I ask you to help me, Please?
>

Redirect the terminal output into a file using standard Linux redirection 
operators.

-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


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[gmx-users] g_dist

[mohammad agha]

Dear Justin, 


Thank you very much from your answer.
May I ask you to help me more, Please?
I work with UBUNTU, I don't know how should I do it!

Best Regards
Sara




On 5/10/13 11:27 AM, mohammad agha wrote:
> Dear GROMACS Specialists,
> I have one problem with g_dist. When I use g_dist along with option -dist, 
> the output is printed on the terminal, but I want them into a file as 
> separately.
> May I ask you to help me, Please?
>

Redirect the terminal output into a file using standard Linux redirection 
operators.

-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



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Re: [gmx-users] g_dist

[Justin Lemkul]

On 5/10/13 11:27 AM, mohammad agha wrote:

Dear GROMACS Specialists,
I have one problem with g_dist. When I use g_dist along with option -dist, the 
output is printed on the terminal, but I want them into a file as separately.
May I ask you to help me, Please?



Redirect the terminal output into a file using standard Linux redirection 
operators.

-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


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[gmx-users] g_dist

[mohammad agha]

Dear GROMACS Specialists,
I have one problem with g_dist. When I use g_dist along with option -dist, the 
output is printed on the terminal, but I want them into a file as separately. 
May I ask you to help me, Please?

Thank you in advance
Best Regards
Sara
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R: Re: [gmx-users] g_dist explanation

[Shilpi Chaurasia]

Thanks for the explanation. I should have used apt values for nstxtcout to get 
what I want. 
Thanks again

Shilpi
Il 23.04.12, "Justin A. Lemkul"   ha scritto:
> 
> 
> On 4/23/12 10:59 AM, Shilpi Chaurasia wrote:
> >  Hi Gromacs users,
> >
> >I am using pull code to separate two units of a protein dimer. I have run the
> >pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where 
> >the
> >data is printed at every 0.01 ps (according to pull_nstxout & pull_nstfout, 
> >both
> >are 10 in this case) as given below
> >
> >0.  0.000322052
> >0.0100  0.173534
> >0.0200  0.297454
> >0.0300  0.416585
> >0.0400  0.519195
> >0.0500  0.597541
> >...
> >
> >Now, I want to calculate the distance between COM of two groups using g_dist 
> >and
> >printing the output data in the same time steps as in .xvg files. I tried but
> >the output data is printed at every 2ps steps as following:
> >
> >    0.000    8.0175037   -0.0010343   -0.0055513    8.0175018
> >    2.000    8.0188007   -0.0202498   -0.0114326    8.0187674
> >    4.000    8.0377693   -0.0229554   -0.0129814    8.0377254
> >    6.000    8.0435743   -0.0226321   -0.0043244    8.0435410
> >    8.000    8.0615864   -0.0312104   -0.0116682    8.0615177
> >...
> >
> >command used
> >g_dist -f  *.xtc -s *.tpr -n index.ndx -o dist.xvg -b 0 -dt 1 -e 650
> >
> >I have also tried by using different values for 'dt' but it doesn't help.
> >If someone could tell me how to control the time steps in g_dist output, in 
> >this
> >case I want the output to be printed in the steps of 0.01 ps
> >
> 
> You can't print frames that aren't there.  If you saved frames using 
> "nstxtcout = 1000" (assuming a time step of 2 fs), then you can't create 
> frames in between.  You would need to do the run again, saving frames with 
> greater frequency. Note that doing so will likely make your trajectory file 
> quite a bit larger.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
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Re: [gmx-users] g_dist explanation

[Justin A. Lemkul]

On 4/23/12 10:59 AM, Shilpi Chaurasia wrote:

  Hi Gromacs users,

I am using pull code to separate two units of a protein dimer. I have run the
pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the
data is printed at every 0.01 ps (according to pull_nstxout & pull_nstfout, both
are 10 in this case) as given below

0.  0.000322052
0.0100  0.173534
0.0200  0.297454
0.0300  0.416585
0.0400  0.519195
0.0500  0.597541
...

Now, I want to calculate the distance between COM of two groups using g_dist and
printing the output data in the same time steps as in .xvg files. I tried but
the output data is printed at every 2ps steps as following:

0.0008.0175037   -0.0010343   -0.00555138.0175018
2.0008.0188007   -0.0202498   -0.01143268.0187674
4.0008.0377693   -0.0229554   -0.01298148.0377254
6.0008.0435743   -0.0226321   -0.00432448.0435410
8.0008.0615864   -0.0312104   -0.01166828.0615177
...

command used
g_dist -f  *.xtc -s *.tpr -n index.ndx -o dist.xvg -b 0 -dt 1 -e 650

I have also tried by using different values for 'dt' but it doesn't help.
If someone could tell me how to control the time steps in g_dist output, in this
case I want the output to be printed in the steps of 0.01 ps



You can't print frames that aren't there.  If you saved frames using "nstxtcout 
= 1000" (assuming a time step of 2 fs), then you can't create frames in between. 
 You would need to do the run again, saving frames with greater frequency. 
Note that doing so will likely make your trajectory file quite a bit larger.


-Justin

--


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


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RE: [gmx-users] g_dist explanation

[Marzinek, Jan]

But the best would be to grompp (NPT) windows (lets say every 10-20 frames) of 
your configuration and at the end of grompp you will see the actual distance 
the gromacs will consider.

Jan



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Shilpi Chaurasia [shilpi.chaura...@unimi.it]
Sent: Monday, April 23, 2012 3:59 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] g_dist explanation

 Hi Gromacs users,

I am using pull code to separate two units of a protein dimer. I have run the 
pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the 
data is printed at every 0.01 ps (according to pull_nstxout & pull_nstfout, 
both are 10 in this case) as given below

0.  0.000322052
0.0100  0.173534
0.0200  0.297454
0.0300  0.416585
0.0400  0.519195
0.0500  0.597541
...

Now, I want to calculate the distance between COM of two groups using g_dist 
and printing the output data in the same time steps as in .xvg files. I tried 
but the output data is printed at every 2ps steps as following:

   0.0008.0175037   -0.0010343   -0.00555138.0175018
   2.0008.0188007   -0.0202498   -0.01143268.0187674
   4.0008.0377693   -0.0229554   -0.01298148.0377254
   6.0008.0435743   -0.0226321   -0.00432448.0435410
   8.0008.0615864   -0.0312104   -0.01166828.0615177
...

command used
g_dist -f  *.xtc -s *.tpr -n index.ndx -o dist.xvg -b 0 -dt 1 -e 650

I have also tried by using different values for 'dt' but it doesn't help.
If someone could tell me how to control the time steps in g_dist output, in 
this case I want the output to be printed in the steps of 0.01 ps

thanks,
Shilpi
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RE: [gmx-users] g_dist explanation

[Marzinek, Jan]

Use trjconv -skip first for your trajcetory so you can rewrite it every 
frame/time step you want. Then proceed to g_dist.

Jan



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Shilpi Chaurasia [shilpi.chaura...@unimi.it]
Sent: Monday, April 23, 2012 3:59 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] g_dist explanation

 Hi Gromacs users,

I am using pull code to separate two units of a protein dimer. I have run the 
pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the 
data is printed at every 0.01 ps (according to pull_nstxout & pull_nstfout, 
both are 10 in this case) as given below

0.  0.000322052
0.0100  0.173534
0.0200  0.297454
0.0300  0.416585
0.0400  0.519195
0.0500  0.597541
...

Now, I want to calculate the distance between COM of two groups using g_dist 
and printing the output data in the same time steps as in .xvg files. I tried 
but the output data is printed at every 2ps steps as following:

   0.0008.0175037   -0.0010343   -0.00555138.0175018
   2.0008.0188007   -0.0202498   -0.01143268.0187674
   4.0008.0377693   -0.0229554   -0.01298148.0377254
   6.0008.0435743   -0.0226321   -0.00432448.0435410
   8.0008.0615864   -0.0312104   -0.01166828.0615177
...

command used
g_dist -f  *.xtc -s *.tpr -n index.ndx -o dist.xvg -b 0 -dt 1 -e 650

I have also tried by using different values for 'dt' but it doesn't help.
If someone could tell me how to control the time steps in g_dist output, in 
this case I want the output to be printed in the steps of 0.01 ps

thanks,
Shilpi
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[gmx-users] g_dist explanation

[Thomas Schlesier]

?Hi Gromacs users,

I am using pull code to separate two units of a protein dimer. I have run the 
pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the data 
is printed at every 0.01 ps (according to pull_nstxout&  pull_nstfout, both are 
10 in this case) as given below

0.? 0.000322052
0.0100? 0.173534
0.0200? 0.297454
0.0300? 0.416585
0.0400? 0.519195
0.0500? 0.597541
...

Now, I want to calculate the distance between COM of two groups using g_dist 
and printing the output data in the same time steps as in .xvg files. I tried 
but the output data is printed at every 2ps steps as following:

?? 0.000??? 8.0175037?? -0.0010343?? -0.0055513??? 8.0175018
?? 2.000??? 8.0188007?? -0.0202498?? -0.0114326??? 8.0187674
?? 4.000??? 8.0377693?? -0.0229554?? -0.0129814??? 8.0377254
?? 6.000??? 8.0435743?? -0.0226321?? -0.0043244??? 8.0435410
?? 8.000??? 8.0615864?? -0.0312104?? -0.0116682??? 8.0615177
...

command used
g_dist -f? *.xtc -s *.tpr -n index.ndx -o dist.xvg -b 0 -dt 1 -e 650

I have also tried by using different values for 'dt' but it doesn't help.
If someone could tell me how to control the time steps in g_dist output, in 
this case I want the output to be printed in the steps of 0.01 ps

thanks,
Shilpi


pull_nstxout and pull_nstfout are only relevant for pullx.xvg and pullx.xvg.
To control the output in *.trr and *.xtc (and therefore for g_dist and 
most other analysis tools) you need to adjust:

nstxout (for *.trr)
nstxtcout (for *.xtc)

Greetings
Thomas
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[gmx-users] g_dist explanation

[Shilpi Chaurasia]

 Hi Gromacs users,

I am using pull code to separate two units of a protein dimer. I have run the 
pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the 
data is printed at every 0.01 ps (according to pull_nstxout & pull_nstfout, 
both are 10 in this case) as given below 

0.  0.000322052
0.0100  0.173534
0.0200  0.297454
0.0300  0.416585
0.0400  0.519195
0.0500  0.597541
...

Now, I want to calculate the distance between COM of two groups using g_dist 
and printing the output data in the same time steps as in .xvg files. I tried 
but the output data is printed at every 2ps steps as following:

   0.000    8.0175037   -0.0010343   -0.0055513    8.0175018
   2.000    8.0188007   -0.0202498   -0.0114326    8.0187674
   4.000    8.0377693   -0.0229554   -0.0129814    8.0377254
   6.000    8.0435743   -0.0226321   -0.0043244    8.0435410
   8.000    8.0615864   -0.0312104   -0.0116682    8.0615177
...

command used 
g_dist -f  *.xtc -s *.tpr -n index.ndx -o dist.xvg -b 0 -dt 1 -e 650

I have also tried by using different values for 'dt' but it doesn't help. 
If someone could tell me how to control the time steps in g_dist output, in 
this case I want the output to be printed in the steps of 0.01 ps

thanks,
Shilpi
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Re: [gmx-users] g_dist without output file

[afsaneh maleki]

On 3/10/12, lina  wrote:
> On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian
>  wrote:
>> Dear Lina
>>
>> There is not any things related to list of atoms on the terminal.
>
> Might your distance -dist so large.
>
> try a smaller one and see.
>>
>>
>> Best regards
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Re: [gmx-users] g_dist without output file

[Mark Abraham]

On 11/03/2012 6:38 PM, Atila Petrosian wrote:

Dear Lina

Very thanks for your time and attention.

Initial command was : g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5

After running following command the problem was solved :

g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 5

t: 17008  6773 NA 21881 NA  3.05534 (nm)
t: 17008  6774 NA 21882 NA  3.27381 (nm)
t: 17008  6775 NA 21883 NA  2.44312 (nm)
t: 17008  6776 NA 21884 NA  2.0746 (nm)
Last frame  2 time 17008.000


Now, I have a general question. In some of gromacs tools, there is
distance parameter.

I want to know what is dimension of the distance in gromacs? nm or A?


See manual section 2.2. Unfortunately, g_dist -dist is one of the places 
where the units are not redundantly specified in the g_dist -h help output.


Mark
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[gmx-users] g_dist without output file

[Atila Petrosian]

Dear Lina

Very thanks for your time and attention.

Initial command was : g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5

After running following command the problem was solved :

g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 5

t: 17008  6773 NA 21881 NA  3.05534 (nm)
t: 17008  6774 NA 21882 NA  3.27381 (nm)
t: 17008  6775 NA 21883 NA  2.44312 (nm)
t: 17008  6776 NA 21884 NA  2.0746 (nm)
Last frame  2 time 17008.000


Now, I have a general question. In some of gromacs tools, there is
distance parameter.

I want to know what is dimension of the distance in gromacs? nm or A?

Best regards
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Re: [gmx-users] g_dist without output file

[lina]

On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian
 wrote:
> Dear Lina
>
> There is not any things related to list of atoms on the terminal.

Might your distance -dist so large.

try a smaller one and see.
>
>
> Best regards
> --
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Re: [gmx-users] g_dist without output file

[lina]

On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian
 wrote:
> Dear Lina
>
> There is not any things related to list of atoms on the terminal.


t: 100  83 ILE 845 CG1  1.60274 (nm)
t: 100  83 ILE 846 CG2  1.63838 (nm)
t: 100  83 ILE 847 CD  1.59769 (nm)
t: 100  83 ILE 848 C  1.8202 (nm)
t: 100  83 ILE 849 O  1.86972 (nm)
t: 100  84 ALA 850 N  1.88309 (nm)
t: 100  84 ALA 851 H  1.85958 (nm)
t: 100  84 ALA 853 CB  1.99705 (nm)
Last frame 50 time  100.000

gcq#310: "Shoot them the atom now" (The Ramones)

g_dist_g -f try_1.xtc -s try_1.tpr -dt 5 -b 0 -e 100 -dist 2 -n index_1.ndx

>
>
> Best regards
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[gmx-users] g_dist without output file

[Atila Petrosian]

Dear Lina

There is not any things related to list of atoms on the terminal.


Best regards
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Re: [gmx-users] g_dist without output file

[lina]

On Sat, Mar 10, 2012 at 9:17 PM, Atila Petrosian
 wrote:
> Dear Lina
>
> Thanks for your reply.
>
> Without the -dist 0.5, I get the -o dist.xvg output, but I need list
> of the all atoms in group 2 closer than dist to the center of mass of
> group 1.

It print on the terminal, you may notice it.

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[gmx-users] g_dist without output file

[Atila Petrosian]

Dear Lina

Thanks for your reply.

Without the -dist 0.5, I get the -o dist.xvg output, but I need list
of the all atoms in group 2 closer than dist to the center of mass of
group 1.
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Re: [gmx-users] g_dist without output file

[lina]

On Sat, Mar 10, 2012 at 7:14 PM, Atila Petrosian
 wrote:
> Dear all
>
> When I use  g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5,
> program was done without error, but it don't create output file
> (dist.xvg) in the directory in which g_dist tool was run.
>
> What is reason of this case?

Try without the -dist 0.5, you will get the -o dist.xvg output.

the -dist is Print all atoms in group 2 closer than dist to
the center of mass of group 1


>
>
> Any help will highly appreciated.
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[gmx-users] g_dist without output file

[Atila Petrosian]

Dear all

When I use  g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5,
program was done without error, but it don't create output file
(dist.xvg) in the directory in which g_dist tool was run.

What is reason of this case?


Any help will highly appreciated.
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[gmx-users] g_dist lifetime option

[Markus Weingarth]

Dear gromacs users,I have a comprehension question to g_dist with the lifetime(-lt) option.I want to determine the lifetime of a certain sidechain - ion contact (I use all ions as a group) within a radis of 0.6 nm.output:@    title "a_538 - K within 0.6 nm"@    xaxis  label "Time (ps)"@    yaxis  label "Number of contacts"@TYPE xy 0.000  1.183   200.000  1.088   400.000  1.048   600.000  1.024   800.000  1.000  1000.000  0.975  1200.000  0.958  1400.000  0.941  1600.000  0.924  1800.000  0.906  2000.000  0.888  2200.000  0.870  2400.000  0.851  2600.000  0.832  2800.000  0.812  3000.000  0.793  3200.000  0.773  3400.000  0.752etc.I have difficulties in understanding why the number of contacts decreases to below zero, though at least one ion is constantly within a raidus of 0.6 nm. Is this a correlation function? Is it possible to look up how this is calculated here?this says the help option :With options -lt and -dist the number of contacts
of all atoms in group 2 that are closer than a certain distance
to the center of mass of group 1 are plotted as a function of the time
that the contact was continously present.Thank you very much.Markus  Ihr WEB.DE Postfach immer dabei: die kostenlose WEB.DE Mail App für iPhone und Android.   https://produkte.web.de/freemail_mobile_startseite/

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Re: [gmx-users] g_dist

[Justin A. Lemkul]

Steven Neumann wrote:

Dear gmx Users,
 
Can you please clarify me as I cannot find it anywhere what means the s0 
legent in the dist.xvg as an outcome from g_dist? What is stated by |d| 
? sx, sy, sz is the vector from two groups obviously.
 


It is the distance.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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_dist

[dina dusti]

Dear Prof.

Thank you very much from your help.

Best Regards
Dina
--
On 3/02/2012 3:17 AM, dina dusti wrote:
> Dear Prof
>
> Thank you very much from your response.
> She said me:
> "In g_dist, when you select two groups for distance calculation, it 
> computes the distance between COM's of groups. Now, what is expected 
> for the distance between the micelle's COM and the COM of (e.g.) head 
> groups? Clearly, it's near zero ! So you should first calculate the 
> distance for each group separately and then average over all distances."
>
> But I didn't understand what was her mean about "you should first 
> calculate the distance for each group separately and then average over 
> all distances.", because I did g_dist between micelle and for example 
> head group and then used g_analyze for dist.xvg and I had the quantity 
> near zero!!!
>

This can be done more efficiently with g_bond, treating each 
head-to-tail distance as a "bond".

Mark-- 
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Re: [gmx-users] g_dist

[Mark Abraham]

On 3/02/2012 3:17 AM, dina dusti wrote:

Dear Prof

Thank you very much from your response.
She said me:
"In g_dist, when you select two groups for distance calculation, it 
computes the distance between COM's of groups. Now, what is expected 
for the distance between the micelle's COM and the COM of (e.g.) head 
groups? Clearly, it's near zero ! So you should first calculate the 
distance for each group separately and then average over all distances."


But I didn't understand what was her mean about "you should first 
calculate the distance for each group separately and then average over 
all distances.", because I did g_dist between micelle and for example 
head group and then used g_analyze for dist.xvg and I had the quantity 
near zero!!!




This can be done more efficiently with g_bond, treating each 
head-to-tail distance as a "bond".


Mark
-- 
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[gmx-users] g_dist

[dina dusti]

Dear Prof.

Thank you very much from your help.

Best Regards
Dina
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Re: [gmx-users] g_dist

[Justin A. Lemkul]

dina dusti wrote:

Dear Prof

Thank you very much from your response.
She said me:
"In g_dist, when you select two groups for distance calculation, it 
computes the distance between COM's of groups. Now, what is expected for 
the distance between the micelle's COM and the COM of (e.g.) head 
groups? Clearly, it's near zero ! So you should first calculate the 
distance for each group separately and then average over all distances."


But I didn't understand what was her mean about "you should first 
calculate the distance for each group separately and then average over 
all distances.", because I did g_dist between micelle and for example 
head group and then used g_analyze for dist.xvg and I had the quantity 
near zero!!!




Which is precisely what she told you.  Her suggestion is to measure the 
head-tail distance of each molecule separately, then average.  This will require 
a large number of index groups (2 groups per molecule, multiplied by however 
many molecules you have to deal with) and will be very tedious, but it can be 
done in this manner.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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_dist

[dina dusti]

Dear Prof

Thank you very much from your response.
She said me:

"In g_dist, when you select two groups for distance calculation, it 
computes the distance between COM's of groups. Now, what is expected for the 
distance between the micelle's COM and the COM of (e.g.) head 
groups? Clearly, it's near zero ! So you should first calculate the 
distance for each group separately and then average over all distances."

But I didn't understand what was her mean about "you should first calculate the 
distance for each group separately and then average over all distances.", 
because I did g_dist between micelle and for example head group and then used 
g_analyze for dist.xvg and I had the quantity near zero!!!

Best Regards
Dina




 From: Justin A. Lemkul 
To: dina dusti ; Discussion list for GROMACS users 
 
Sent: Thursday, February 2, 2012 6:07 PM
Subject: Re: [gmx-users] g_dist
 


dina dusti wrote:
> Dear Prof.
> 
> Thank you very much from your response.
> Yes, I contacted with one of them and she said me use g_dist, but I have 
> problem with it.
> 

Perhaps she could be more specific.  Obviously whatever you're doing with 
g_dist is not working, and I honestly can't think of a way to make g_dist 
produce anything I would call a "root-mean-square distance."

-Justin

> Thank you again because of your patient.
> Best Regards
> Dina
> 
> 
> *From:* Justin A. Lemkul 
> *To:* dina dusti ; Discussion list for GROMACS users 
> 
> *Sent:* Thursday, February 2, 2012 2:42 PM
> *Subject:* Re: [gmx-users] g_dist
> 
> 
> 
> dina dusti wrote:
>  > Dear Prof.
>  >
>  > Thank you very much from your response.
>  > OK, I use from g_gyrate for all of radius, but I still don't understand 
>that what thing did they use in their articles for root-mean-square distance 
>because they compared this quantity with quantity of obtained from gyration!!!
>  >
> 
> It's hard for anyone to speculate about an article that we haven't read.  The 
> best course of action is to contact the corresponding author and ask for 
> additional information.  Based on what you learn there, you can apply similar 
> analyses.
> 
> -Justin
> 
>  > Thank you again.
>  > Best Regards
>  > Dina
>  >
>  > 
>  > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
>  > *To:* dina dusti mailto:dinadu...@yahoo.com>>; 
>Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>>
>  > *Sent:* Thursday, February 2, 2012 12:08 AM
>  > *Subject:* Re: [gmx-users] g_dist
>  >
>  >
>  >
>  > dina dusti wrote:
>  >  > Dear Prof.
>  >  >
>  >  > Thank you very much from your response.
>  >  > He answer me that I should use from g_gyration for radius of micelle, 
>but what should I do for hydrocarbon (dry) core or calculation of inner core 
>of micelle (i.e. the first of carbon on tail of surfactant with COM of 
>micelle)?
>  >  >
>  >
>  > Use g_gyrate, with a custom index group that contains the atoms of 
>interest.  If you're interested in the radius of the hydrocarbon atoms, make 
>that an index group and perform the analysis on it.
>  >
>  > -Justin
>  >
>  > -- 
>  >
>  > Justin A. Lemkul
>  > Ph.D. Candidate
>  > ICTAS Doctoral Scholar
>  > MILES-IGERT Trainee
>  > Department of Biochemistry
>  > Virginia Tech
>  > Blacksburg, VA
>  > jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) 231-9080
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
>  > 
>  >
>  >
> 
> -- 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> 
> 

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] g_dist

[Justin A. Lemkul]

dina dusti wrote:

Dear Prof.

Thank you very much from your response.
Yes, I contacted with one of them and she said me use g_dist, but I have 
problem with it.




Perhaps she could be more specific.  Obviously whatever you're doing with g_dist 
is not working, and I honestly can't think of a way to make g_dist produce 
anything I would call a "root-mean-square distance."


-Justin


Thank you again because of your patient.
Best Regards
Dina


*From:* Justin A. Lemkul 
*To:* dina dusti ; Discussion list for GROMACS 
users 

*Sent:* Thursday, February 2, 2012 2:42 PM
*Subject:* Re: [gmx-users] g_dist



dina dusti wrote:
 > Dear Prof.
 >
 > Thank you very much from your response.
 > OK, I use from g_gyrate for all of radius, but I still don't 
understand that what thing did they use in their articles for 
root-mean-square distance because they compared this quantity with 
quantity of obtained from gyration!!!

 >

It's hard for anyone to speculate about an article that we haven't 
read.  The best course of action is to contact the corresponding author 
and ask for additional information.  Based on what you learn there, you 
can apply similar analyses.


-Justin

 > Thank you again.
 > Best Regards
 > Dina
 >
 > 
 > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
 > *To:* dina dusti mailto:dinadu...@yahoo.com>>; 
Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>>

 > *Sent:* Thursday, February 2, 2012 12:08 AM
 > *Subject:* Re: [gmx-users] g_dist
 >
 >
 >
 > dina dusti wrote:
 >  > Dear Prof.
 >  >
 >  > Thank you very much from your response.
 >  > He answer me that I should use from g_gyration for radius of 
micelle, but what should I do for hydrocarbon (dry) core or calculation 
of inner core of micelle (i.e. the first of carbon on tail of surfactant 
with COM of micelle)?

 >  >
 >
 > Use g_gyrate, with a custom index group that contains the atoms of 
interest.  If you're interested in the radius of the hydrocarbon atoms, 
make that an index group and perform the analysis on it.

 >
 > -Justin
 >
 > -- 
 >
 > Justin A. Lemkul
 > Ph.D. Candidate
 > ICTAS Doctoral Scholar
 > MILES-IGERT Trainee
 > Department of Biochemistry
 > Virginia Tech
 > Blacksburg, VA
 > jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 > 
 >
 >

-- 

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






--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
Please search the archive at 
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[gmx-users] g_dist

[dina dusti]

Dear Prof.

Thank you very much from your response.
Yes, I contacted with one of them and she said me use g_dist, but I have 
problem with it.

Thank you again because of your patient.
Best Regards
Dina




 From: Justin A. Lemkul 
To: dina dusti ; Discussion list for GROMACS users 
 
Sent: Thursday, February 2, 2012 2:42 PM
Subject: Re: [gmx-users] g_dist
 


dina dusti wrote:
> Dear Prof.
> 
> Thank you very much from your response.
> OK, I use from g_gyrate for all of radius, but I still don't understand that 
> what thing did they use in their articles for root-mean-square distance 
> because they compared this quantity with quantity of obtained from gyration!!!
> 

It's hard for anyone to speculate about an article that we haven't read.  The 
best course of action is to contact the corresponding author and ask for 
additional information.  Based on what you learn there, you can apply similar 
analyses.

-Justin

> Thank you again.
> Best Regards
> Dina
> 
> 
> *From:* Justin A. Lemkul 
> *To:* dina dusti ; Discussion list for GROMACS users 
> 
> *Sent:* Thursday, February 2, 2012 12:08 AM
> *Subject:* Re: [gmx-users] g_dist
> 
> 
> 
> dina dusti wrote:
>  > Dear Prof.
>  >
>  > Thank you very much from your response.
>  > He answer me that I should use from g_gyration for radius of micelle, but 
>what should I do for hydrocarbon (dry) core or calculation of inner core of 
>micelle (i.e. the first of carbon on tail of surfactant with COM of micelle)?
>  >
> 
> Use g_gyrate, with a custom index group that contains the atoms of interest.  
> If you're interested in the radius of the hydrocarbon atoms, make that an 
> index group and perform the analysis on it.
> 
> -Justin
> 
> -- 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> 
> 

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] g_dist

[Justin A. Lemkul]

dina dusti wrote:

Dear Prof.

Thank you very much from your response.
OK, I use from g_gyrate for all of radius, but I still don't understand 
that what thing did they use in their articles for root-mean-square 
distance because they compared this quantity with quantity of obtained 
from gyration!!!




It's hard for anyone to speculate about an article that we haven't read.  The 
best course of action is to contact the corresponding author and ask for 
additional information.  Based on what you learn there, you can apply similar 
analyses.


-Justin


Thank you again.
Best Regards
Dina


*From:* Justin A. Lemkul 
*To:* dina dusti ; Discussion list for GROMACS 
users 

*Sent:* Thursday, February 2, 2012 12:08 AM
*Subject:* Re: [gmx-users] g_dist



dina dusti wrote:
 > Dear Prof.
 >
 > Thank you very much from your response.
 > He answer me that I should use from g_gyration for radius of micelle, 
but what should I do for hydrocarbon (dry) core or calculation of inner 
core of micelle (i.e. the first of carbon on tail of surfactant with COM 
of micelle)?

 >

Use g_gyrate, with a custom index group that contains the atoms of 
interest.  If you're interested in the radius of the hydrocarbon atoms, 
make that an index group and perform the analysis on it.


-Justin

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin






--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
Please search the archive at 
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[gmx-users] g_dist

[dina dusti]

Dear Prof.

Thank you very much from your response.
OK, I use from g_gyrate for all of radius, but I still don't understand that 
what thing did they use in their articles for root-mean-square distance because 
they compared this quantity with quantity of obtained from gyration!!!

Thank you again.
Best Regards
Dina




 From: Justin A. Lemkul 
To: dina dusti ; Discussion list for GROMACS users 
 
Sent: Thursday, February 2, 2012 12:08 AM
Subject: Re: [gmx-users] g_dist
 


dina dusti wrote:
> Dear Prof.
> 
> Thank you very much from your response.
> He answer me that I should use from g_gyration for radius of micelle, but 
> what should I do for hydrocarbon (dry) core or calculation of inner core of 
> micelle (i.e. the first of carbon on tail of surfactant with COM of micelle)?
> 

Use g_gyrate, with a custom index group that contains the atoms of interest.  
If you're interested in the radius of the hydrocarbon atoms, make that an index 
group and perform the analysis on it.

-Justin

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
Please search the archive at 
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Re: [gmx-users] g_dist

[Justin A. Lemkul]

dina dusti wrote:

Dear Prof.

Thank you very much from your response.
He answer me that I should use from g_gyration for radius of micelle, 
but what should I do for hydrocarbon (dry) core or calculation of inner 
core of micelle (i.e. the first of carbon on tail of surfactant with COM 
of micelle)?




Use g_gyrate, with a custom index group that contains the atoms of interest.  If 
you're interested in the radius of the hydrocarbon atoms, make that an index 
group and perform the analysis on it.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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_dist

[dina dusti]

Dear Prof.

Thank you very much from your response.

He answer me that I should use from g_gyration for radius of micelle, but what 
should I do for hydrocarbon (dry) core or calculation of inner core of micelle 
(i.e. the first of carbon on tail of surfactant with COM of micelle)?

Best Regards
Dina
-- 
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Re: [gmx-users] g_dist

[Justin A. Lemkul]

dina dusti wrote:

Dear Prof.

Thank you very much for your help.
Yes, I also used from g_rdf and g_gyrate but I am seeking 
"root-mean-square distance" that there is in many articles for 
calculation of radius of micelle and radius of dry core (hydrocarbone). 
I understood that they used g_dist but it doesn't work me. Perhaps I am 
wrong about required program (command) for calculation of 
root-mean-square distance?


Didn't Tsjerk already answer this?

http://lists.gromacs.org/pipermail/gmx-users/2012-January/067984.html

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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_dist

[dina dusti]

Dear Prof.

Thank you very much for your help.
Yes, I also used from g_rdf and g_gyrate but I am seeking "root-mean-square 
distance" that there is in many articles for calculation of radius of micelle 
and radius of dry core (hydrocarbone). I understood that they used g_dist but 
it doesn't work me. Perhaps I am wrong about required program (command) for 
calculation of root-mean-square distance?
Please help me.
Thank you again.

Best Regards
Dina  




 From: Justin A. Lemkul 
To: dina dusti ; Discussion list for GROMACS users 
 
Sent: Wednesday, February 1, 2012 9:15 PM
Subject: Re: [gmx-users] g_dist
 


dina dusti wrote:
> Dear Prof.
> 
> Thank you very much from your response.
> but I didn't select micelle headgroups and then terminal carbon atom but also 
> I selected COM of micelle and for example head group of micelle! The 
> calulation of radius of micelle by radius of gyration give that is near 
> 2.3-2.4 nm but g_dist ...!!!

g_dist and g_gyrate work in different ways.  You can't equate their output.

A micelle is (roughly) a sphere.  The COM of the headgroups will be the center 
of the sphere.  Thus, the COM of the micelle is the COM of the sphere and the 
COM of the headgroups is (approximately) coincident.  Hence why you are getting 
a very tiny distance reported by g_dist.

> Where is my mistake?
> I select groups in index file correctly.
> Please help me.
> 

g_rdf might be a better option, by selecting the COM of the micelle as the 
reference and the headgroups as the group for calculation.  That way you will 
get the distribution of headgroup distances from the COM of the micelle, thus 
approximately the radius of the micelle.

-Justin

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Re: [gmx-users] g_dist

[Justin A. Lemkul]

dina dusti wrote:

Dear Prof.

Thank you very much from your response.
but I didn't select micelle headgroups and then terminal carbon atom but 
also I selected COM of micelle and for example head group of micelle! 
The calulation of radius of micelle by radius of gyration give that is 
near 2.3-2.4 nm but g_dist ...!!!


g_dist and g_gyrate work in different ways.  You can't equate their output.

A micelle is (roughly) a sphere.  The COM of the headgroups will be the center 
of the sphere.  Thus, the COM of the micelle is the COM of the sphere and the 
COM of the headgroups is (approximately) coincident.  Hence why you are getting 
a very tiny distance reported by g_dist.



Where is my mistake?
I select groups in index file correctly.
Please help me.



g_rdf might be a better option, by selecting the COM of the micelle as the 
reference and the headgroups as the group for calculation.  That way you will 
get the distribution of headgroup distances from the COM of the micelle, thus 
approximately the radius of the micelle.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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_dist

[dina dusti]

Dear Prof.

Thank you very much from your response.
I removed pbc and jump in my system, and when I see my system as visual in 
ngmx, there is not pbc and jump and has been created one micelle and it remain 
stable for long times. 
I really don't know what should I do!

Best Regards
Dina
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[gmx-users] g_dist

[dina dusti]

Dear Prof.


Thank you very much from your response.
but I didn't select micelle headgroups and then terminal carbon atom but also I 
selected COM of micelle and for example head group of micelle! The calulation 
of radius of micelle by radius of gyration give that is near 2.3-2.4 nm but 
g_dist ...!!!
Where is my mistake?
I select groups in index file correctly.
Please help me.

Thank you again.
Best Regards
Dina  




 From: Justin A. Lemkul 
To: dina dusti ; Discussion list for GROMACS users 
 
Sent: Wednesday, February 1, 2012 3:13 PM
Subject: Re: [gmx-users] g_dist
 


dina dusti wrote:
> Dear Prof.
> 
> Thank you very much from your response.
> Yes, dist.xvg has four column consists origin distance and distances in 
> direction x, y , z. So distance that I want according to result of g_analyze, 
> is 5.324286e-02 that isn't correct. I selected 2 groups, micelle and the last 
> carbon bounded with head group for index file.
> Also, I did this job for micelle and head group, and micelle with other 
> groups but my results (distances) were all of them near the zero.
> Please help me to obtain correct distance.
> 

Keep in mind what g_dist is measuring, center-of-mass distances.  If you select 
the micelle headgroups and then terminal carbon atoms, the positions will be 
almost coincident, as your result suggests.  Other groups that are giving a 
nearly-zero distance are likely coincident in the same manner.

-Justin

-- 

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

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Re: [gmx-users] g_dist

[Justin A. Lemkul]

dina dusti wrote:

Dear Prof.

Thank you very much from your response.
Yes, dist.xvg has four column consists origin distance and distances in 
direction x, y , z. So distance that I want according to result of 
g_analyze, is 5.324286e-02 that isn't correct. I selected 2 groups, 
micelle and the last carbon bounded with head group for index file.
Also, I did this job for micelle and head group, and micelle with other 
groups but my results (distances) were all of them near the zero.

Please help me to obtain correct distance.



Keep in mind what g_dist is measuring, center-of-mass distances.  If you select 
the micelle headgroups and then terminal carbon atoms, the positions will be 
almost coincident, as your result suggests.  Other groups that are giving a 
nearly-zero distance are likely coincident in the same manner.


-Justin

--


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


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Re: [gmx-users] g_dist

[Mark Abraham]

On 1/02/2012 4:26 PM, dina dusti wrote:

Dear Prof.

Thank you very much from your response.
Yes, dist.xvg has four column consists origin distance and distances 
in direction x, y , z. So distance that I want according to result of 
g_analyze, is 5.324286e-02 that isn't correct. I selected 2 groups, 
micelle and the last carbon bounded with head group for index file.
Also, I did this job for micelle and head group, and micelle with 
other groups but my results (distances) were all of them near the zero.

Please help me to obtain correct distance.



If your groups are correct and g_dist is correct and your simulation 
conforms to your expectation of micelle structure then at least one of 
the foregoing isn't true. You may have a periodicity artefact (see 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions 
for how to avoid if so). You may have no micelle. Your groups may be wrong.


Mark
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[gmx-users] g_dist

[dina dusti]

Dear Prof.

Thank you very much from your response. 

Yes, dist.xvg has four column consists origin distance and distances in 
direction x, y , z. So distance that I want according to result of g_analyze, 
is 5.324286e-02 that isn't correct. I selected 2 groups, micelle and the last 
carbon bounded with head group for index file.
Also, I did this job for micelle and head group, and micelle with other groups 
but my results (distances) were all of them near the zero.
Please help me to obtain correct distance.

Thank you again.
Best Regards
Dina  
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Re: [gmx-users] g_dist

[Mark Abraham]

On 1/02/2012 1:05 AM, dina dusti wrote:

Dear Gromacs specialists,

Can you help me about g_dist?
I have a micelle system, I want to obtain distance between center of 
mass of micelle with the last of carbon bounded to head group in 
surfactant.
It should be near 2.2 but when I did   "g_dist -f md.xtc -s md.tpr -b 
15 -o dist.xvg" and then selected micelle and the last carbon 
bounded to head group, respectively , and  next did "g_analyze -f 
dist.xvg -av" it give me :

  std. dev.relative deviation of
   standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
  cum. 3   cum. 4
SS1   5.324286e-02   2.182349e-02   3.984406e-04   0.2870.064
SS2  -2.000683e-04   3.327947e-02   6.075972e-04   0.045   -0.036
SS3  -6.405102e-04   3.270624e-02   5.971315e-04   0.001   -0.052
SS4  -2.96e-04   3.366480e-02   6.146323e-04   0.016   -0.013

What should I do for obtain correct distance?



You've analyzed a data set with four distributions, but you'll have to 
go back to the column labels of dist.xvg to work out how to interpret 
the statistics of each distribution. It looks to me like your index 
groups are not the ones you thought they were.


Mark
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[gmx-users] g_dist

[dina dusti]

Dear Gromacs specialists,

Can you help me about g_dist?
I have a micelle system, I want to obtain distance between center of mass of 
micelle with the last of carbon bounded to head group in surfactant. 

It should be near 2.2 but when I did   "g_dist -f md.xtc -s md.tpr -b 15 -o 
dist.xvg" and then selected micelle and the last carbon bounded to head group, 
respectively , and  next did "g_analyze -f dist.xvg -av" it give me : 
  std. dev.    relative deviation of
   standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
  cum. 3   cum. 4
SS1   5.324286e-02   2.182349e-02   3.984406e-04   0.287    0.064
SS2  -2.000683e-04   3.327947e-02   6.075972e-04   0.045   -0.036
SS3  -6.405102e-04   3.270624e-02   5.971315e-04   0.001   -0.052
SS4  -2.96e-04   3.366480e-02   6.146323e-04   0.016   -0.013


What should I do for obtain correct distance? 


Best Regards
Dina
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Re: [gmx-users] g_dist error

[Thomas Schlesier]

never used the -dist option, but i think you have here a missunderstanding:

>>> t: 275  20230 SOL 62618 OW  0.341434 (nm)

i think this means: at time=275 atom 62618 (which is a OW) from residue 
20230 (which is a SOL) is 0.341434nm away from your protein atom.


the x SOL y OW means not the distance between some SOl-atom and OW, but 
that the OW atom is from the residue x from the SOL group!!!



>>> And when am already specifying only one atom from protein ie say 
1322. why

>>> do i get this kind of output-
>>> t: 275  20230 SOL 62618 OW  0.341434 (nm)
>>> t: 275  22019 SOL 67985 OW  0.171584 (nm)
>>> t: 276  10768 SOL 34232 OW  0.303328 (nm)
>>> t: 276  20230 SOL 62618 OW  0.325176 (nm)
...

you get this output, because the programm assumes that you remember 
which was group 1 and so it does not need to write it in every line.


since i never used the -dist option, the stuff above could be false, so 
short thing you can do is and look if atom 62618 is in residue 20230, 
and then the above should be right.


greetings
thomas




Date: Tue, 13 Sep 2011 13:32:26 +0530
From: aiswarya pawar
Subject: Re: [gmx-users] g_dist error
To: Discussion list for GROMACS users
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 if the index name not given it
takes the default index file, so there isnt any wrong in selecting the
atoms.

On Tue, Sep 13, 2011 at 1:24 PM, Mark Abrahamwrote:


  On 13/09/2011 4:14 PM, aiswarya pawar wrote:

Mark,

the command line goes like this-

g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500


This command line is not using an index file. The index groups defined for
the grompp that produced the .tpr are being used (which may be the default
ones, depending what you did). Please copy and show the interactive input
you made to g_dist after it showed the groups it knew about.



the index file has group1- a_1322 ( this is just a single atom from a
protein. its in sidechain)
   group2- a_OW ( this is water atoms)


Your output is listing the time of the frame, and the residue number,
residue name, atom number, and atom name of the matching atom. Apparently a
water molecule can sometimes be closer than 0.2nm, and sometimes not.

Mark



now as per the utility it should give me and output as-

t:1 1322 a 54119 OW 0.389

but am getting something different

On Tue, Sep 13, 2011 at 11:24 AM, Mark Abrahamwrote:


  On 13/09/2011 3:40 PM, aiswarya pawar wrote:


Hi Mark,

The -dist option says- print all the atoms in group 2 that are closer than
a certain distance to the center of mass of group 1.
That means it should give me the distance from OW to protein atom.


  If you choose correct groups that are correctly defined with respect to
your trajectory and use a large enough distance cutoff.



And when am already specifying only one atom from protein ie say 1322. why
do i get this kind of output-


  We can't tell. We don't know what your command line is, what's in your
simulation system, the contents of your index groups, or which groups you've
selected for which role. Clearly something is not working properly, and our
time constraints mean that we're going to assume you've done something
wrong, in the absence of evidence to the contrary.

Mark



t: 275  20230 SOL 62618 OW  0.341434 (nm)
t: 275  22019 SOL 67985 OW  0.171584 (nm)
t: 276  10768 SOL 34232 OW  0.303328 (nm)
t: 276  20230 SOL 62618 OW  0.325176 (nm)
t: 276  22019 SOL 67985 OW  0.187259 (nm)
t: 277  10768 SOL 34232 OW  0.306008 (nm)
t: 277  20230 SOL 62618 OW  0.326195 (nm)
t: 277  22019 SOL 67985 OW  0.181089 (nm)
t: 278  10768 SOL 34232 OW  0.274507 (nm)
t: 278  22019 SOL 67985 OW  0.292652 (nm)
t: 279  10618 SOL 33782 OW  0.319922 (nm)
t: 280  10618 SOL 33782 OW  0.330082 (nm)
t: 280  22019 SOL 67985 OW  0.330203 (nm)
t: 281  8273 SOL 26747 OW  0.278731 (nm)
t: 281  10618 SOL 33782 OW  0.325434 (nm)
t: 281  11535 SOL 36533 OW  0.200327 (nm)
t: 281  17036 SOL 53036 OW  0.343946 (nm)
t: 282  8273 SOL 26747 OW  0.256558 (nm)
t: 282  11535 SOL 36533 OW  0.327147 (nm)
t: 283  8273 SOL 26747 OW  0.165061 (nm)
t: 283  10618 SOL 33782 OW  0.306578 (nm)
t: 283  17191 SOL 53501 OW  0.333075 (nm)
t: 284  8273 SOL 26747 OW  0.19427 (nm)
t: 284  10618 SOL 33782 OW  0.321927 (nm)
t: 284  17191 SOL 53501 OW  0.30832 (nm)




On Tue, Sep 13, 2011 at 10:40 AM, Mark Abrahamwrote:


  On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote:

Iam -dist option because I need the distance between two groups


  That is not what g_dist -dist does. Please read g_dist -h.


   excluding -dist gives me X,Y,Z output which I don't want.


  And other output which you do, but you have to use -o to get it. Read
g_dist -h.


   And am not specifying an -o.


  You need to specify -o to achieve your purpose. However, as I said quite
a while ago, there is no value in measu

Re: [gmx-users] g_dist error

[aiswarya pawar]

g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 if the index name not given it
takes the default index file, so there isnt any wrong in selecting the
atoms.

On Tue, Sep 13, 2011 at 1:24 PM, Mark Abraham wrote:

>  On 13/09/2011 4:14 PM, aiswarya pawar wrote:
>
> Mark,
>
> the command line goes like this-
>
> g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500
>
>
> This command line is not using an index file. The index groups defined for
> the grompp that produced the .tpr are being used (which may be the default
> ones, depending what you did). Please copy and show the interactive input
> you made to g_dist after it showed the groups it knew about.
>
>
>
> the index file has group1- a_1322 ( this is just a single atom from a
> protein. its in sidechain)
>   group2- a_OW ( this is water atoms)
>
>
> Your output is listing the time of the frame, and the residue number,
> residue name, atom number, and atom name of the matching atom. Apparently a
> water molecule can sometimes be closer than 0.2nm, and sometimes not.
>
> Mark
>
>
>
> now as per the utility it should give me and output as-
>
> t:1 1322 a 54119 OW 0.389
>
> but am getting something different
>
> On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham wrote:
>
>>  On 13/09/2011 3:40 PM, aiswarya pawar wrote:
>>
>>
>> Hi Mark,
>>
>> The -dist option says- print all the atoms in group 2 that are closer than
>> a certain distance to the center of mass of group 1.
>> That means it should give me the distance from OW to protein atom.
>>
>>
>>  If you choose correct groups that are correctly defined with respect to
>> your trajectory and use a large enough distance cutoff.
>>
>>
>>
>> And when am already specifying only one atom from protein ie say 1322. why
>> do i get this kind of output-
>>
>>
>>  We can't tell. We don't know what your command line is, what's in your
>> simulation system, the contents of your index groups, or which groups you've
>> selected for which role. Clearly something is not working properly, and our
>> time constraints mean that we're going to assume you've done something
>> wrong, in the absence of evidence to the contrary.
>>
>> Mark
>>
>>
>>
>> t: 275  20230 SOL 62618 OW  0.341434 (nm)
>> t: 275  22019 SOL 67985 OW  0.171584 (nm)
>> t: 276  10768 SOL 34232 OW  0.303328 (nm)
>> t: 276  20230 SOL 62618 OW  0.325176 (nm)
>> t: 276  22019 SOL 67985 OW  0.187259 (nm)
>> t: 277  10768 SOL 34232 OW  0.306008 (nm)
>> t: 277  20230 SOL 62618 OW  0.326195 (nm)
>> t: 277  22019 SOL 67985 OW  0.181089 (nm)
>> t: 278  10768 SOL 34232 OW  0.274507 (nm)
>> t: 278  22019 SOL 67985 OW  0.292652 (nm)
>> t: 279  10618 SOL 33782 OW  0.319922 (nm)
>> t: 280  10618 SOL 33782 OW  0.330082 (nm)
>> t: 280  22019 SOL 67985 OW  0.330203 (nm)
>> t: 281  8273 SOL 26747 OW  0.278731 (nm)
>> t: 281  10618 SOL 33782 OW  0.325434 (nm)
>> t: 281  11535 SOL 36533 OW  0.200327 (nm)
>> t: 281  17036 SOL 53036 OW  0.343946 (nm)
>> t: 282  8273 SOL 26747 OW  0.256558 (nm)
>> t: 282  11535 SOL 36533 OW  0.327147 (nm)
>> t: 283  8273 SOL 26747 OW  0.165061 (nm)
>> t: 283  10618 SOL 33782 OW  0.306578 (nm)
>> t: 283  17191 SOL 53501 OW  0.333075 (nm)
>> t: 284  8273 SOL 26747 OW  0.19427 (nm)
>> t: 284  10618 SOL 33782 OW  0.321927 (nm)
>> t: 284  17191 SOL 53501 OW  0.30832 (nm)
>>
>>
>>
>>
>> On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham 
>> wrote:
>>
>>>  On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote:
>>>
>>> Iam -dist option because I need the distance between two groups
>>>
>>>
>>>  That is not what g_dist -dist does. Please read g_dist -h.
>>>
>>>
>>>   excluding -dist gives me X,Y,Z output which I don't want.
>>>
>>>
>>>  And other output which you do, but you have to use -o to get it. Read
>>> g_dist -h.
>>>
>>>
>>>   And am not specifying an -o.
>>>
>>>
>>>  You need to specify -o to achieve your purpose. However, as I said quite
>>> a while ago, there is no value in measuring the distance between a protein
>>> phase and a water phase if they are in contact...
>>>
>>> Mark
>>>
>>>
>>>  Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
>>> it!
>>>
>>> -Original Message-
>>> From: "Justin A. Lemkul"  
>>> Date: Mon,

Re: [gmx-users] g_dist error

[Mark Abraham]

On 13/09/2011 4:14 PM, aiswarya pawar wrote:

Mark,

the command line goes like this-

g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500


This command line is not using an index file. The index groups defined 
for the grompp that produced the .tpr are being used (which may be the 
default ones, depending what you did). Please copy and show the 
interactive input you made to g_dist after it showed the groups it knew 
about.




the index file has group1- a_1322 ( this is just a single atom from a 
protein. its in sidechain)

  group2- a_OW ( this is water atoms)


Your output is listing the time of the frame, and the residue number, 
residue name, atom number, and atom name of the matching atom. 
Apparently a water molecule can sometimes be closer than 0.2nm, and 
sometimes not.


Mark



now as per the utility it should give me and output as-

t:1 1322 a 54119 OW 0.389

but am getting something different

On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham 
mailto:mark.abra...@anu.edu.au>> wrote:


On 13/09/2011 3:40 PM, aiswarya pawar wrote:


Hi Mark,

The -dist option says- print all the atoms in group 2 that are
closer than a certain distance to the center of mass of group 1.
That means it should give me the distance from OW to protein atom.


If you choose correct groups that are correctly defined with
respect to your trajectory and use a large enough distance cutoff.




And when am already specifying only one atom from protein ie say
1322. why do i get this kind of output-


We can't tell. We don't know what your command line is, what's in
your simulation system, the contents of your index groups, or
which groups you've selected for which role. Clearly something is
not working properly, and our time constraints mean that we're
going to assume you've done something wrong, in the absence of
evidence to the contrary.

Mark




t: 275  20230 SOL 62618 OW  0.341434 (nm)
t: 275  22019 SOL 67985 OW  0.171584 (nm)
t: 276  10768 SOL 34232 OW  0.303328 (nm)
t: 276  20230 SOL 62618 OW  0.325176 (nm)
t: 276  22019 SOL 67985 OW  0.187259 (nm)
t: 277  10768 SOL 34232 OW  0.306008 (nm)
t: 277  20230 SOL 62618 OW  0.326195 (nm)
t: 277  22019 SOL 67985 OW  0.181089 (nm)
t: 278  10768 SOL 34232 OW  0.274507 (nm)
t: 278  22019 SOL 67985 OW  0.292652 (nm)
t: 279  10618 SOL 33782 OW  0.319922 (nm)
t: 280  10618 SOL 33782 OW  0.330082 (nm)
t: 280  22019 SOL 67985 OW  0.330203 (nm)
t: 281  8273 SOL 26747 OW  0.278731 (nm)
t: 281  10618 SOL 33782 OW  0.325434 (nm)
t: 281  11535 SOL 36533 OW  0.200327 (nm)
t: 281  17036 SOL 53036 OW  0.343946 (nm)
t: 282  8273 SOL 26747 OW  0.256558 (nm)
t: 282  11535 SOL 36533 OW  0.327147 (nm)
t: 283  8273 SOL 26747 OW  0.165061 (nm)
t: 283  10618 SOL 33782 OW  0.306578 (nm)
t: 283  17191 SOL 53501 OW  0.333075 (nm)
t: 284  8273 SOL 26747 OW  0.19427 (nm)
t: 284  10618 SOL 33782 OW  0.321927 (nm)
t: 284  17191 SOL 53501 OW  0.30832 (nm)




On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:

On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com
<mailto:aiswarya.pa...@gmail.com> wrote:

Iam -dist option because I need the distance between two groups


That is not what g_dist -dist does. Please read g_dist -h.



  excluding -dist gives me X,Y,Z output which I don't want.


And other output which you do, but you have to use -o to get
it. Read g_dist -h.



  And am not specifying an -o.


You need to specify -o to achieve your purpose. However, as I
said quite a while ago, there is no value in measuring the
distance between a protein phase and a water phase if they
are in contact...

Mark



Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go 
for it!

-Original Message-
From: "Justin A. Lemkul"  <mailto:jalem...@vt.edu>
Date: Mon, 12 Sep 2011 22:35:28
To:  <mailto:aiswarya.pa...@gmail.com>; Discussion list 
for GROMACS users  <mailto:gmx-users@gromacs.org>
    Reply-To:jalem...@vt.edu  <mailto:jalem...@vt.edu>
Subject: Re: [gmx-users] g_dist error



aiswarya.pa...@gmail.com  <mailto:aiswarya.pa...@gmail.com>  wrote:

Even if I specify an atom say 1277 atom number to find distance against 
the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even 
after specifying one atom from a protein why doesn't it give me the result for 
the SOL.



As was suggested several messages ago, please do NOT combine -o and 
-dist.  If
you want to measure a distance, use -o.  If you want g_dist to print a 
list of
atoms that satisfy some given crite

Re: [gmx-users] g_dist error

[aiswarya pawar]

Mark,

the command line goes like this-

g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500

the index file has group1- a_1322 ( this is just a single atom from a
protein. its in sidechain)
  group2- a_OW ( this is water atoms)

now as per the utility it should give me and output as-

t:1 1322 a 54119 OW 0.389

but am getting something different

On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham wrote:

>  On 13/09/2011 3:40 PM, aiswarya pawar wrote:
>
>
> Hi Mark,
>
> The -dist option says- print all the atoms in group 2 that are closer than
> a certain distance to the center of mass of group 1.
> That means it should give me the distance from OW to protein atom.
>
>
> If you choose correct groups that are correctly defined with respect to
> your trajectory and use a large enough distance cutoff.
>
>
>
> And when am already specifying only one atom from protein ie say 1322. why
> do i get this kind of output-
>
>
> We can't tell. We don't know what your command line is, what's in your
> simulation system, the contents of your index groups, or which groups you've
> selected for which role. Clearly something is not working properly, and our
> time constraints mean that we're going to assume you've done something
> wrong, in the absence of evidence to the contrary.
>
> Mark
>
>
>
> t: 275  20230 SOL 62618 OW  0.341434 (nm)
> t: 275  22019 SOL 67985 OW  0.171584 (nm)
> t: 276  10768 SOL 34232 OW  0.303328 (nm)
> t: 276  20230 SOL 62618 OW  0.325176 (nm)
> t: 276  22019 SOL 67985 OW  0.187259 (nm)
> t: 277  10768 SOL 34232 OW  0.306008 (nm)
> t: 277  20230 SOL 62618 OW  0.326195 (nm)
> t: 277  22019 SOL 67985 OW  0.181089 (nm)
> t: 278  10768 SOL 34232 OW  0.274507 (nm)
> t: 278  22019 SOL 67985 OW  0.292652 (nm)
> t: 279  10618 SOL 33782 OW  0.319922 (nm)
> t: 280  10618 SOL 33782 OW  0.330082 (nm)
> t: 280  22019 SOL 67985 OW  0.330203 (nm)
> t: 281  8273 SOL 26747 OW  0.278731 (nm)
> t: 281  10618 SOL 33782 OW  0.325434 (nm)
> t: 281  11535 SOL 36533 OW  0.200327 (nm)
> t: 281  17036 SOL 53036 OW  0.343946 (nm)
> t: 282  8273 SOL 26747 OW  0.256558 (nm)
> t: 282  11535 SOL 36533 OW  0.327147 (nm)
> t: 283  8273 SOL 26747 OW  0.165061 (nm)
> t: 283  10618 SOL 33782 OW  0.306578 (nm)
> t: 283  17191 SOL 53501 OW  0.333075 (nm)
> t: 284  8273 SOL 26747 OW  0.19427 (nm)
> t: 284  10618 SOL 33782 OW  0.321927 (nm)
> t: 284  17191 SOL 53501 OW  0.30832 (nm)
>
>
>
>
> On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham wrote:
>
>>  On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote:
>>
>> Iam -dist option because I need the distance between two groups
>>
>>
>>  That is not what g_dist -dist does. Please read g_dist -h.
>>
>>
>>   excluding -dist gives me X,Y,Z output which I don't want.
>>
>>
>>  And other output which you do, but you have to use -o to get it. Read
>> g_dist -h.
>>
>>
>>   And am not specifying an -o.
>>
>>
>>  You need to specify -o to achieve your purpose. However, as I said quite
>> a while ago, there is no value in measuring the distance between a protein
>> phase and a water phase if they are in contact...
>>
>> Mark
>>
>>
>>  Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
>> it!
>>
>> -Original Message-
>> From: "Justin A. Lemkul"  
>> Date: Mon, 12 Sep 2011 22:35:28
>> To:  ; Discussion list 
>> for GROMACS users 
>> Reply-To: jalem...@vt.edu
>> Subject: Re: [gmx-users] g_dist error
>>
>>
>> aiswarya.pa...@gmail.com wrote:
>>
>>  Even if I specify an atom say 1277 atom number to find distance against the 
>> OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even 
>> after specifying one atom from a protein why doesn't it give me the result 
>> for the SOL.
>>
>>
>>
>>  As was suggested several messages ago, please do NOT combine -o and -dist.  
>> If
>> you want to measure a distance, use -o.  If you want g_dist to print a list 
>> of
>> atoms that satisfy some given criteria, use -dist, but not together.
>>
>> -Justin
>>
>>
>>  Thanks
>> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
>> it!
>>
>> -Original Message-
>> From: "Justin A. Lemkul"  
>> Sender: gmx-users-boun...@gromacs.org
>> Date: Mon, 12 Sep 2011 07:52:54
>> To: Discussion list for GROMACS users 
>> 
>> Reply-To: jalem...@vt.edu,
>>  Discussion list for GROMACS users  
>

Re: [gmx-users] g_dist error

[Mark Abraham]

On 13/09/2011 3:40 PM, aiswarya pawar wrote:


Hi Mark,

The -dist option says- print all the atoms in group 2 that are closer 
than a certain distance to the center of mass of group 1.

That means it should give me the distance from OW to protein atom.


If you choose correct groups that are correctly defined with respect to 
your trajectory and use a large enough distance cutoff.




And when am already specifying only one atom from protein ie say 1322. 
why do i get this kind of output-


We can't tell. We don't know what your command line is, what's in your 
simulation system, the contents of your index groups, or which groups 
you've selected for which role. Clearly something is not working 
properly, and our time constraints mean that we're going to assume 
you've done something wrong, in the absence of evidence to the contrary.


Mark



t: 275  20230 SOL 62618 OW  0.341434 (nm)
t: 275  22019 SOL 67985 OW  0.171584 (nm)
t: 276  10768 SOL 34232 OW  0.303328 (nm)
t: 276  20230 SOL 62618 OW  0.325176 (nm)
t: 276  22019 SOL 67985 OW  0.187259 (nm)
t: 277  10768 SOL 34232 OW  0.306008 (nm)
t: 277  20230 SOL 62618 OW  0.326195 (nm)
t: 277  22019 SOL 67985 OW  0.181089 (nm)
t: 278  10768 SOL 34232 OW  0.274507 (nm)
t: 278  22019 SOL 67985 OW  0.292652 (nm)
t: 279  10618 SOL 33782 OW  0.319922 (nm)
t: 280  10618 SOL 33782 OW  0.330082 (nm)
t: 280  22019 SOL 67985 OW  0.330203 (nm)
t: 281  8273 SOL 26747 OW  0.278731 (nm)
t: 281  10618 SOL 33782 OW  0.325434 (nm)
t: 281  11535 SOL 36533 OW  0.200327 (nm)
t: 281  17036 SOL 53036 OW  0.343946 (nm)
t: 282  8273 SOL 26747 OW  0.256558 (nm)
t: 282  11535 SOL 36533 OW  0.327147 (nm)
t: 283  8273 SOL 26747 OW  0.165061 (nm)
t: 283  10618 SOL 33782 OW  0.306578 (nm)
t: 283  17191 SOL 53501 OW  0.333075 (nm)
t: 284  8273 SOL 26747 OW  0.19427 (nm)
t: 284  10618 SOL 33782 OW  0.321927 (nm)
t: 284  17191 SOL 53501 OW  0.30832 (nm)




On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham 
mailto:mark.abra...@anu.edu.au>> wrote:


On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com
<mailto:aiswarya.pa...@gmail.com> wrote:

Iam -dist option because I need the distance between two groups


That is not what g_dist -dist does. Please read g_dist -h.



  excluding -dist gives me X,Y,Z output which I don't want.


And other output which you do, but you have to use -o to get it.
Read g_dist -h.



  And am not specifying an -o.


You need to specify -o to achieve your purpose. However, as I said
quite a while ago, there is no value in measuring the distance
between a protein phase and a water phase if they are in contact...

Mark



Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
it!

-Original Message-
From: "Justin A. Lemkul"  <mailto:jalem...@vt.edu>
Date: Mon, 12 Sep 2011 22:35:28
To:  <mailto:aiswarya.pa...@gmail.com>; Discussion list for 
GROMACS users  <mailto:gmx-users@gromacs.org>
    Reply-To:jalem...@vt.edu  <mailto:jalem...@vt.edu>
Subject: Re: [gmx-users] g_dist error



aiswarya.pa...@gmail.com  <mailto:aiswarya.pa...@gmail.com>  wrote:

Even if I specify an atom say 1277 atom number to find distance against the 
OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even 
after specifying one atom from a protein why doesn't it give me the result for 
the SOL.



As was suggested several messages ago, please do NOT combine -o and -dist.  
If
you want to measure a distance, use -o.  If you want g_dist to print a list 
of
atoms that satisfy some given criteria, use -dist, but not together.

-Justin


Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
it!

-Original Message-
From: "Justin A. Lemkul"  <mailto:jalem...@vt.edu>
Sender:gmx-users-boun...@gromacs.org  <mailto:gmx-users-boun...@gromacs.org>
Date: Mon, 12 Sep 2011 07:52:54
To: Discussion list for GROMACS users  
<mailto:gmx-users@gromacs.org>
Reply-To:jalem...@vt.edu  <mailto:jalem...@vt.edu>,
Discussion list for GROMACS users  
<mailto:gmx-users@gromacs.org>
Subject: Re: [gmx-users] g_dist error



aiswarya pawar wrote:

hi Justin,

As far i referred the OW,HW1 etc are water atoms so how can it be
distance between the SOL protein atoms, instead it is SOL water atoms.


The printed distance indicates that there is a certain water molecule that 
is
just over 2 hydrogen bonding lengths away from your protein's backbone.  
Sounds
normal to me.

-Justin


Thanks

On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkulmailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu>>  wrote:



 aiswarya pawar wrote:

 Hi Users,

 Am using g_dist to find the distance between water 

Re: [gmx-users] g_dist error

[aiswarya pawar]

Hi Mark,

The -dist option says- print all the atoms in group 2 that are closer than a
certain distance to the center of mass of group 1.
That means it should give me the distance from OW to protein atom.

And when am already specifying only one atom from protein ie say 1322. why
do i get this kind of output-

t: 275  20230 SOL 62618 OW  0.341434 (nm)
t: 275  22019 SOL 67985 OW  0.171584 (nm)
t: 276  10768 SOL 34232 OW  0.303328 (nm)
t: 276  20230 SOL 62618 OW  0.325176 (nm)
t: 276  22019 SOL 67985 OW  0.187259 (nm)
t: 277  10768 SOL 34232 OW  0.306008 (nm)
t: 277  20230 SOL 62618 OW  0.326195 (nm)
t: 277  22019 SOL 67985 OW  0.181089 (nm)
t: 278  10768 SOL 34232 OW  0.274507 (nm)
t: 278  22019 SOL 67985 OW  0.292652 (nm)
t: 279  10618 SOL 33782 OW  0.319922 (nm)
t: 280  10618 SOL 33782 OW  0.330082 (nm)
t: 280  22019 SOL 67985 OW  0.330203 (nm)
t: 281  8273 SOL 26747 OW  0.278731 (nm)
t: 281  10618 SOL 33782 OW  0.325434 (nm)
t: 281  11535 SOL 36533 OW  0.200327 (nm)
t: 281  17036 SOL 53036 OW  0.343946 (nm)
t: 282  8273 SOL 26747 OW  0.256558 (nm)
t: 282  11535 SOL 36533 OW  0.327147 (nm)
t: 283  8273 SOL 26747 OW  0.165061 (nm)
t: 283  10618 SOL 33782 OW  0.306578 (nm)
t: 283  17191 SOL 53501 OW  0.333075 (nm)
t: 284  8273 SOL 26747 OW  0.19427 (nm)
t: 284  10618 SOL 33782 OW  0.321927 (nm)
t: 284  17191 SOL 53501 OW  0.30832 (nm)




On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham wrote:

>  On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote:
>
> Iam -dist option because I need the distance between two groups
>
>
> That is not what g_dist -dist does. Please read g_dist -h.
>
>
>   excluding -dist gives me X,Y,Z output which I don't want.
>
>
> And other output which you do, but you have to use -o to get it. Read
> g_dist -h.
>
>
>   And am not specifying an -o.
>
>
> You need to specify -o to achieve your purpose. However, as I said quite a
> while ago, there is no value in measuring the distance between a protein
> phase and a water phase if they are in contact...
>
> Mark
>
>
>  Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
> it!
>
> -Original Message-
> From: "Justin A. Lemkul"  
> Date: Mon, 12 Sep 2011 22:35:28
> To:  ; Discussion list 
> for GROMACS users 
> Reply-To: jalem...@vt.edu
> Subject: Re: [gmx-users] g_dist error
>
>
> aiswarya.pa...@gmail.com wrote:
>
>  Even if I specify an atom say 1277 atom number to find distance against the 
> OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even 
> after specifying one atom from a protein why doesn't it give me the result 
> for the SOL.
>
>
>
>  As was suggested several messages ago, please do NOT combine -o and -dist.  
> If
> you want to measure a distance, use -o.  If you want g_dist to print a list of
> atoms that satisfy some given criteria, use -dist, but not together.
>
> -Justin
>
>
>  Thanks
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
>
> -Original Message-
> From: "Justin A. Lemkul"  
> Sender: gmx-users-boun...@gromacs.org
> Date: Mon, 12 Sep 2011 07:52:54
> To: Discussion list for GROMACS users 
> 
> Reply-To: jalem...@vt.edu,
>   Discussion list for GROMACS users  
> 
> Subject: Re: [gmx-users] g_dist error
>
>
>
> aiswarya pawar wrote:
>
>  hi Justin,
>
> As far i referred the OW,HW1 etc are water atoms so how can it be
> distance between the SOL protein atoms, instead it is SOL water atoms.
>
>
>  The printed distance indicates that there is a certain water molecule that is
> just over 2 hydrogen bonding lengths away from your protein's backbone.  
> Sounds
> normal to me.
>
> -Justin
>
>
>  Thanks
>
> On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul  <mailto:jalem...@vt.edu> > wrote:
>
>
>
> aiswarya pawar wrote:
>
> Hi Users,
>
> Am using g_dist to find the distance between water and protein.
> but my output has the values of SOL-water distance.
>
> t: 1  136 SOL 2336 OW  0.772373 (nm)
>
>
> This is not a water-water distance, it is the output of the -dist
> option telling you that water molecule 136 has its OW atom at
> 0.7723273 nm from whatever your reference group is.
>
> -Justin
>
> --
> ==__==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.__vt.edu/Pag

Re: [gmx-users] g_dist error

[Mark Abraham]

On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote:

Iam -dist option because I need the distance between two groups


That is not what g_dist -dist does. Please read g_dist -h.


  excluding -dist gives me X,Y,Z output which I don't want.


And other output which you do, but you have to use -o to get it. Read 
g_dist -h.



  And am not specifying an -o.


You need to specify -o to achieve your purpose. However, as I said quite 
a while ago, there is no value in measuring the distance between a 
protein phase and a water phase if they are in contact...


Mark



Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: "Justin A. Lemkul"
Date: Mon, 12 Sep 2011 22:35:28
To:; Discussion list for GROMACS 
users
Reply-To: jalem...@vt.edu
Subject: Re: [gmx-users] g_dist error



aiswarya.pa...@gmail.com wrote:

Even if I specify an atom say 1277 atom number to find distance against the OW 
atoms. I get the same result of SOL-OW distance. Is it a bug cause even after 
specifying one atom from a protein why doesn't it give me the result for the 
SOL.



As was suggested several messages ago, please do NOT combine -o and -dist.  If
you want to measure a distance, use -o.  If you want g_dist to print a list of
atoms that satisfy some given criteria, use -dist, but not together.

-Justin


Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: "Justin A. Lemkul"
Sender: gmx-users-boun...@gromacs.org
Date: Mon, 12 Sep 2011 07:52:54
To: Discussion list for GROMACS users
Reply-To: jalem...@vt.edu,
Discussion list for GROMACS users
Subject: Re: [gmx-users] g_dist error



aiswarya pawar wrote:

hi Justin,

As far i referred the OW,HW1 etc are water atoms so how can it be
distance between the SOL protein atoms, instead it is SOL water atoms.


The printed distance indicates that there is a certain water molecule that is
just over 2 hydrogen bonding lengths away from your protein's backbone.  Sounds
normal to me.

-Justin


Thanks

On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkulmailto:jalem...@vt.edu>>  wrote:



 aiswarya pawar wrote:

 Hi Users,

 Am using g_dist to find the distance between water and protein.
 but my output has the values of SOL-water distance.

 t: 1  136 SOL 2336 OW  0.772373 (nm)


 This is not a water-water distance, it is the output of the -dist
 option telling you that water molecule 136 has its OW atom at
 0.7723273 nm from whatever your reference group is.

 -Justin

 --
 ==__==

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu<http://vt.edu>  | (540) 231-9080
 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
 <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>

 ==__==
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Re: [gmx-users] g_dist error

[aiswarya . pawar]

Iam -dist option because I need the distance between two groups, excluding 
-dist gives me X,Y,Z output which I don't want. And am not specifying an -o.

Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: "Justin A. Lemkul" 
Date: Mon, 12 Sep 2011 22:35:28 
To: ; Discussion list for GROMACS 
users
Reply-To: jalem...@vt.edu
Subject: Re: [gmx-users] g_dist error



aiswarya.pa...@gmail.com wrote:
> Even if I specify an atom say 1277 atom number to find distance against the 
> OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even 
> after specifying one atom from a protein why doesn't it give me the result 
> for the SOL.
> 
> 

As was suggested several messages ago, please do NOT combine -o and -dist.  If 
you want to measure a distance, use -o.  If you want g_dist to print a list of 
atoms that satisfy some given criteria, use -dist, but not together.

-Justin

> Thanks
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
> 
> -Original Message-
> From: "Justin A. Lemkul" 
> Sender: gmx-users-boun...@gromacs.org
> Date: Mon, 12 Sep 2011 07:52:54 
> To: Discussion list for GROMACS users
> Reply-To: jalem...@vt.edu,
>   Discussion list for GROMACS users 
> Subject: Re: [gmx-users] g_dist error
> 
> 
> 
> aiswarya pawar wrote:
>> hi Justin,
>>
>> As far i referred the OW,HW1 etc are water atoms so how can it be 
>> distance between the SOL protein atoms, instead it is SOL water atoms.
>>
> 
> The printed distance indicates that there is a certain water molecule that is 
> just over 2 hydrogen bonding lengths away from your protein's backbone.  
> Sounds 
> normal to me.
> 
> -Justin
> 
>> Thanks
>>
>> On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul > <mailto:jalem...@vt.edu>> wrote:
>>
>>
>>
>> aiswarya pawar wrote:
>>
>> Hi Users,
>>
>> Am using g_dist to find the distance between water and protein.
>> but my output has the values of SOL-water distance.
>>
>> t: 1  136 SOL 2336 OW  0.772373 (nm)
>>
>>
>> This is not a water-water distance, it is the output of the -dist
>> option telling you that water molecule 136 has its OW atom at
>> 0.7723273 nm from whatever your reference group is.
>>
>> -Justin
>>
>> -- 
>> ==__==
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==__==
>> -- 
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>> <mailto:gmx-users@gromacs.org>
>> http://lists.gromacs.org/__mailman/listinfo/gmx-users
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> 

-- 


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


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Re: [gmx-users] g_dist error

[Justin A. Lemkul]

aiswarya.pa...@gmail.com wrote:

Even if I specify an atom say 1277 atom number to find distance against the OW 
atoms. I get the same result of SOL-OW distance. Is it a bug cause even after 
specifying one atom from a protein why doesn't it give me the result for the 
SOL.




As was suggested several messages ago, please do NOT combine -o and -dist.  If 
you want to measure a distance, use -o.  If you want g_dist to print a list of 
atoms that satisfy some given criteria, use -dist, but not together.


-Justin


Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: "Justin A. Lemkul" 
Sender: gmx-users-boun...@gromacs.org
Date: Mon, 12 Sep 2011 07:52:54 
To: Discussion list for GROMACS users

Reply-To: jalem...@vt.edu,
Discussion list for GROMACS users 
Subject: Re: [gmx-users] g_dist error



aiswarya pawar wrote:

hi Justin,

As far i referred the OW,HW1 etc are water atoms so how can it be 
distance between the SOL protein atoms, instead it is SOL water atoms.




The printed distance indicates that there is a certain water molecule that is 
just over 2 hydrogen bonding lengths away from your protein's backbone.  Sounds 
normal to me.


-Justin


Thanks

On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote:




aiswarya pawar wrote:

Hi Users,

Am using g_dist to find the distance between water and protein.
but my output has the values of SOL-water distance.

t: 1  136 SOL 2336 OW  0.772373 (nm)


This is not a water-water distance, it is the output of the -dist
option telling you that water molecule 136 has its OW atom at
0.7723273 nm from whatever your reference group is.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>

==__==
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--


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


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Re: [gmx-users] g_dist error

[aiswarya . pawar]

Even if I specify an atom say 1277 atom number to find distance against the OW 
atoms. I get the same result of SOL-OW distance. Is it a bug cause even after 
specifying one atom from a protein why doesn't it give me the result for the 
SOL.


Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: "Justin A. Lemkul" 
Sender: gmx-users-boun...@gromacs.org
Date: Mon, 12 Sep 2011 07:52:54 
To: Discussion list for GROMACS users
Reply-To: jalem...@vt.edu,
Discussion list for GROMACS users 
Subject: Re: [gmx-users] g_dist error



aiswarya pawar wrote:
> hi Justin,
> 
> As far i referred the OW,HW1 etc are water atoms so how can it be 
> distance between the SOL protein atoms, instead it is SOL water atoms.
> 

The printed distance indicates that there is a certain water molecule that is 
just over 2 hydrogen bonding lengths away from your protein's backbone.  Sounds 
normal to me.

-Justin

> Thanks
> 
> On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul  <mailto:jalem...@vt.edu>> wrote:
> 
> 
> 
> aiswarya pawar wrote:
> 
> Hi Users,
> 
> Am using g_dist to find the distance between water and protein.
> but my output has the values of SOL-water distance.
> 
> t: 1  136 SOL 2336 OW  0.772373 (nm)
> 
> 
> This is not a water-water distance, it is the output of the -dist
> option telling you that water molecule 136 has its OW atom at
> 0.7723273 nm from whatever your reference group is.
> 
> -Justin
> 
> -- 
> ==__==
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
> ==__==
> -- 
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> <mailto:gmx-users@gromacs.org>
> http://lists.gromacs.org/__mailman/listinfo/gmx-users
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> Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
> <http://www.gromacs.org/Support/Mailing_Lists>
> 
> 

-- 


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


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Re: [gmx-users] g_dist error

[Justin A. Lemkul]

aiswarya pawar wrote:

hi Justin,

As far i referred the OW,HW1 etc are water atoms so how can it be 
distance between the SOL protein atoms, instead it is SOL water atoms.




The printed distance indicates that there is a certain water molecule that is 
just over 2 hydrogen bonding lengths away from your protein's backbone.  Sounds 
normal to me.


-Justin


Thanks

On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul > wrote:




aiswarya pawar wrote:

Hi Users,

Am using g_dist to find the distance between water and protein.
but my output has the values of SOL-water distance.

t: 1  136 SOL 2336 OW  0.772373 (nm)


This is not a water-water distance, it is the output of the -dist
option telling you that water molecule 136 has its OW atom at
0.7723273 nm from whatever your reference group is.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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--


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


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Re: [gmx-users] g_dist error

[Justin A. Lemkul]

aiswarya pawar wrote:

Hi Justin,

Am using g_dist to find the distance between water and protein. for that i made 
a index file such as-

a CA(protein atoms)

a OW(water atoms)

i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35



instead of getting the result for protein-SOL distance . my output shows SOL-OW 
distance as seen below-

t: 1  136 SOL 2336 OW  0.772373 (nm)
 
even after specifying am getting an wrong output.




I don't know why this shows up if you're using "-dist 0.35" but it still sounds 
like you're going about your task the wrong way.  If you want the distance 
between CA atoms and water as a function of time, leave off -dist and the output 
you want is in the dist.xvg file written by g_dist (-o output option).  This 
will be a relatively insensitive measurement and you will probably need better 
index groups.


-Justin



Thanks



On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul > wrote:




aiswarya pawar wrote:

Hi Users,

Am using g_dist to find the distance between water and protein.
but my output has the values of SOL-water distance.

t: 1  136 SOL 2336 OW  0.772373 (nm)


This is not a water-water distance, it is the output of the -dist
option telling you that water molecule 136 has its OW atom at
0.7723273 nm from whatever your reference group is.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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--


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


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Re: [gmx-users] g_dist output error

[aiswarya pawar]

hi Justin,

As far i referred the OW,HW1 etc are water atoms so how can it be distance
between the SOL protein atoms, instead it is SOL water atoms.

Thanks

On Mon, Sep 12, 2011 at 4:53 PM, Justin A. Lemkul  wrote:

>
>
> aiswarya pawar wrote:
>
>> Hi gromacs Users,
>>
>> Am using g_dist to find the distance between water and protein. for that i
>> made a index file such as-
>>
>> a CA(protein atoms)
>>
>> a OW(water atoms)
>>
>> i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist
>> 0.35
>>
>>
>> instead of getting the result for protein-SOL distance . my output shows
>> SOL-OW distance as seen below-
>>
>> t: 1  136 SOL 2336 OW  0.772373 (nm)
>>  can anyone tell me whats wrong with this.
>>
>
> Please see my previous message.  This is not a "SOL-water" distance.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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Re: [gmx-users] g_dist error

[aiswarya pawar]

hi Justin,

As far i referred the OW,HW1 etc are water atoms so how can it be distance
between the SOL protein atoms, instead it is SOL water atoms.

Thanks

On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul  wrote:

>
>
> aiswarya pawar wrote:
>
>> Hi Users,
>>
>> Am using g_dist to find the distance between water and protein. but my
>> output has the values of SOL-water distance.
>>
>> t: 1  136 SOL 2336 OW  0.772373 (nm)
>>
>>
> This is not a water-water distance, it is the output of the -dist option
> telling you that water molecule 136 has its OW atom at 0.7723273 nm from
> whatever your reference group is.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  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
>
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Re: [gmx-users] g_dist error

[aiswarya pawar]

Hi Justin,

Am using g_dist to find the distance between water and protein. for
that i made a index file such as-

a CA(protein atoms)

a OW(water atoms)

i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35


instead of getting the result for protein-SOL distance . my output
shows SOL-OW distance as seen below-

t: 1  136 SOL 2336 OW  0.772373 (nm)

even after specifying am getting an wrong output.

Thanks



On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul  wrote:

>
>
> aiswarya pawar wrote:
>
>> Hi Users,
>>
>> Am using g_dist to find the distance between water and protein. but my
>> output has the values of SOL-water distance.
>>
>> t: 1  136 SOL 2336 OW  0.772373 (nm)
>>
>>
> This is not a water-water distance, it is the output of the -dist option
> telling you that water molecule 136 has its OW atom at 0.7723273 nm from
> whatever your reference group is.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  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
>
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Re: [gmx-users] g_dist output error

[Justin A. Lemkul]

aiswarya pawar wrote:

Hi gromacs Users,

Am using g_dist to find the distance between water and protein. for that i made 
a index file such as-

a CA(protein atoms)

a OW(water atoms)

i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35


instead of getting the result for protein-SOL distance . my output shows SOL-OW 
distance as seen below-

t: 1  136 SOL 2336 OW  0.772373 (nm)
 can anyone tell me whats wrong with this.


Please see my previous message.  This is not a "SOL-water" distance.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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[gmx-users] g_dist output error

[aiswarya pawar]

Hi gromacs Users,

Am using g_dist to find the distance between water and protein. for
that i made a index file such as-

a CA(protein atoms)

a OW(water atoms)

i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35

instead of getting the result for protein-SOL distance . my output
shows SOL-OW distance as seen below-

t: 1  136 SOL 2336 OW  0.772373 (nm)
 can anyone tell me whats wrong with this.
Thanks
-- 
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!
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Re: [gmx-users] g_dist error

[Justin A. Lemkul]

aiswarya pawar wrote:

Hi Users,

Am using g_dist to find the distance between water and protein. but my 
output has the values of SOL-water distance.


t: 1  136 SOL 2336 OW  0.772373 (nm)



This is not a water-water distance, it is the output of the -dist option telling 
you that water molecule 136 has its OW atom at 0.7723273 nm from whatever your 
reference group is.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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_dist error

[aiswarya pawar]

Hi Users,

Am using g_dist to find the distance between water and protein. but my
output has the values of SOL-water distance.

t: 1  136 SOL 2336 OW  0.772373 (nm)

Thanks
-- 
gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] g_dist with multiple chains of molecules

[Mark Abraham]

On 15/07/2011 6:37 AM, Sanku M wrote:

Hi,
  I am running a simulation where I have 100 chains of molecule in a 
box . I am trying to calculate the distance between two particular 
atoms ( present in each molecule)  averaged over all the chains of 
molecule. i.e If I have atom C1 and C2 in each of the molecule-chain, 
I want to calculate the distance between C1 and C2 atom in each chain 
and average over them.
I was trying to use gromacs 4.0.7  g_dist tool . For that, I first 
created two  index-groups  of all C1 and C2 . But. I realized that 
g_dist will give me actually the distance between center of mass of 
all C1 and center of mass of all C2 which is NOT certainly I was 
looking for.
 So, I was wondering whether there is any other tool which can split 
the entire index group by deviding it by total number of chains and 
then calculate each individual distances for each chain and then do an 
average over them.


Check out g_dist -h. There are some other tools suggested there that 
look at inter-group distances in a different ways, and one of them works 
well for you.


Mark

An analogous tool exists for g_gyrate where where one can use -nmol 
option to split the entire index accordingly and calculate the radius 
of gyration averaged over all the molecules. I was looking for 
something for calculating distances between two atoms for many chain 
molecules.


I looked at the mailing list but I could not find any solutions for 
these. Any help will be appreciated.


Sanku


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Re: [gmx-users] g_dist with multiple chains of molecules

[Justin A. Lemkul]

Sanku M wrote:

Hi,
  I am running a simulation where I have 100 chains of molecule in a box 
. I am trying to calculate the distance between two particular atoms ( 
present in each molecule)  averaged over all the chains of molecule. i.e 
If I have atom C1 and C2 in each of the molecule-chain, I want to 
calculate the distance between C1 and C2 atom in each chain and average 
over them.
I was trying to use gromacs 4.0.7  g_dist tool . For that, I first 
created two  index-groups  of all C1 and C2 . But. I realized that 
g_dist will give me actually the distance between center of mass of all 
C1 and center of mass of all C2 which is NOT certainly I was looking for.
 So, I was wondering whether there is any other tool which can split the 
entire index group by deviding it by total number of chains and then 
calculate each individual distances for each chain and then do an 
average over them.




You can split the group within make_ndx.  There are various splitting keywords 
(like 'splitat' or 'splitres') that can divide up your index groups.  Then 
script the 100 calls to g_dist.


-Justin



An analogous tool exists for g_gyrate where where one can use -nmol 
option to split the entire index accordingly and calculate the radius of 
gyration averaged over all the molecules. I was looking for something 
for calculating distances between two atoms for many chain molecules.


I looked at the mailing list but I could not find any solutions for 
these. Any help will be appreciated.


Sanku
 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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_dist with multiple chains of molecules

[Sanku M]

Hi,
  I am running a simulation where I have 100 chains of molecule in a box . I am 
trying to calculate the distance between two particular atoms ( present in each 
molecule)  averaged over all the chains of molecule. i.e If I have atom C1 and 
C2 in each of the molecule-chain, I want to calculate the distance between C1 
and C2 atom in each chain and average over them.
I was trying to use gromacs 4.0.7  g_dist tool . For that, I first created two 
 index-groups  of all C1 and C2 . But. I realized that g_dist will give me 
actually the distance between center of mass of all C1 and center of mass of 
all 
C2 which is NOT certainly I was looking for.
 So, I was wondering whether there is any other tool which can split the entire 
index group by deviding it by total number of chains and then calculate each 
individual distances for each chain and then do an average over them.


An analogous tool exists for g_gyrate where where one can use -nmol option to 
split the entire index accordingly and calculate the radius of gyration 
averaged 
over all the molecules. I was looking for something for calculating distances 
between two atoms for many chain molecules.

I looked at the mailing list but I could not find any solutions for these. Any 
help will be appreciated.

Sanku-- 
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[gmx-users] g_dist

[chris . neale]

Dear Nilesh:

You don't seem to have made any progress since Mark gave you some  
reading hints. Your best chance to get a useful response follows the  
general form:


1. I want to do A.
2. I tried method B, here are the exact commands that I used (copy and paste)
3. With that method, I obtain C
4. But I am confused about why C does not look like D.
5. What is the problem?

Basically, it helps to show that you are doing your own work too.

For example, try a command on a single frame and then look at that  
frame with VMD and count for yourself and verify the answer that way.


Chris.

-- original message --

I have a system with 128 emi (cations) and 128 Cl (anions).

I want to calculate how many CL atoms are in cutoff distance relative to
hydorgen aotm of cation.  I considered all CL atoms are distinguishable.

Basically I want to calcualte the distance between each CL atom and
correponing hydorgen and registered those CL atoms which are whthin
cutoff.

How can I do ?

I am using Gromacs 4.0.7 version.

Thanks

Nilesh










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[gmx-users] g_dist

[Nilesh Dhumal]

Hello,

I have a system with 128 emi (cations) and 128 Cl (anions).

I want to calculate how many CL atoms are in cutoff distance relative to
hydorgen aotm of cation.  I considered all CL atoms are distinguishable.

Basically I want to calcualte the distance between each CL atom and
correponing hydorgen and registered those CL atoms which are whthin
cutoff.

How can I do ?

I am using Gromacs 4.0.7 version.

Thanks

Nilesh








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Re: [gmx-users] g_dist issue( Out put file)

[Justin A. Lemkul]

tekle...@ualberta.ca wrote:

Dear Justine,

I got it and works fine.

@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.7047197   -0.3054392   -0.15599120.6156325
19002.0000.7591453   -0.2601027   -0.26593630.6617599
19004.0000.7763510   -0.3043177   -0.22149120.6790090
19006.0000.7837191   -0.2325068   -0.26536930.6998110
=

I have another question for you. Does g_analyse is oky to use to get the 
mean separation.




I don't see why not.  That's pretty much the main function of g_analyze.


g_anayze -f .xvg -av average.xvg -errbar enum -b 19000 -e 2

is the column 1 and two is correct means time and distance respectively.



Per the notation in the .xvg file, yes.


=


Is the same process apply for the g-rdf?

 Group 0 (  System) has 28708 elements

Group 1 ( PAP) has   512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has20 elements


I want to calculate g(r) for PAP molecules.. but by default it is 
there does I need to create two PAP_1 and PAP_2 to get the g(r). To get 
for the


PAP-PAP g(r) value. Or just need to select 1 twice?


Try it and see :)

-Justin



Rob


Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

Dear Justine,
Reading file PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr, VERSION 3.3.3 
(single precision)

Group 0 (  System) has 28708 elements
Group 1 ( PAP) has   512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has20 elements
Select a group: 3
Selected 3: 'RING'
Select a group: 3
Selected 3: 'RING'
Reading frame   0 time 19000.000
Back Off! I just backed up DistPAP8HEP.xvg to ./#DistPAP8HEP.xvg.8#
Last frame500 time 2.000



which means I have to create two index file for two rings Ring_1 AND 
Ring_2 and choose both of them. If I am correct.




Yes.  Otherwise the distance from the center of mass of RING is 
calculated relative to the center of mass of RING, which by definition 
will always be zero.


-Justin


Rob




Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

The following is the out put.

# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 
-o DistPAP8HEP.xvg

#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@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 "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.0000.0000.0000.000
19002.0000.0000.0000.0000.000
19004.0000.0000.0000.0000.000
19006.0000.0000.0000.0000.000
19008.0000.0000.0000.0000.000
19010.0000.0000.0000.0000.000
19012.0000.0000.0000.0000.000
19014.0000.0000.0000.0000.000
19016.0000.0000.0000.0000.000
19018.0000.0000.0000.0000.000
19020.0000.0000.0000.0000.000
19022.0000.0000.0000.0000.000
19024.0000.0000.0000.0000.000
19026.0000.0000.0000.0000.000
19028.0000.0000.0000.0000.000
19030.0000.0000.0000.0000.000
19032.0000.0000.0



You say you want the distance between two rings, but you only showed 
an index group for one of them (presumably), and the fact that 
you've gotten all zeroes as a result would suggest that you chose 
the same group twice for the distance calculation.  Which groups did 
you select?  Do they correspond to two, non-overlapping index groups?


-Justin




Quoting tekle...@ualberta.ca:


Dear Gromacs users,

I run my simulation for 20ns and want to extract aromatic-aromatic 
distance to see the stacking issue. But I am unable to get the value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
 123456789   10   11   12   13   
14   15
16   17   18   19   20   21   22   23   24   25   26   27   28   
29   30
31   32   33   34   35   36   37   38   39   40   41   42   43   
44   45
46   47   48   49   50   51   52   53   54   55   56   57   58   
59   6

Re: [gmx-users] g_dist issue( Out put file)

[teklebrh]

Dear Justine,

I got it and works fine.

@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.7047197   -0.3054392   -0.15599120.6156325
19002.0000.7591453   -0.2601027   -0.26593630.6617599
19004.0000.7763510   -0.3043177   -0.22149120.6790090
19006.0000.7837191   -0.2325068   -0.26536930.6998110
=

I have another question for you. Does g_analyse is oky to use to get  
the mean separation.


g_anayze -f .xvg -av average.xvg -errbar enum -b 19000 -e 2

is the column 1 and two is correct means time and distance respectively.

=


Is the same process apply for the g-rdf?

 Group 0 (  System) has 28708 elements

Group 1 ( PAP) has   512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has20 elements


I want to calculate g(r) for PAP molecules.. but by default it is  
there does I need to create two PAP_1 and PAP_2 to get the g(r). To  
get for the


PAP-PAP g(r) value. Or just need to select 1 twice?

Rob


Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

Dear Justine,
Reading file PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr, VERSION 3.3.3  
(single precision)

Group 0 (  System) has 28708 elements
Group 1 ( PAP) has   512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has20 elements
Select a group: 3
Selected 3: 'RING'
Select a group: 3
Selected 3: 'RING'
Reading frame   0 time 19000.000
Back Off! I just backed up DistPAP8HEP.xvg to ./#DistPAP8HEP.xvg.8#
Last frame500 time 2.000



which means I have to create two index file for two rings Ring_1  
AND Ring_2 and choose both of them. If I am correct.




Yes.  Otherwise the distance from the center of mass of RING is  
calculated relative to the center of mass of RING, which by  
definition will always be zero.


-Justin


Rob




Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

The following is the out put.

# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e  
2 -o DistPAP8HEP.xvg

#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@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 "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.0000.0000.0000.000
19002.0000.0000.0000.0000.000
19004.0000.0000.0000.0000.000
19006.0000.0000.0000.0000.000
19008.0000.0000.0000.0000.000
19010.0000.0000.0000.0000.000
19012.0000.0000.0000.0000.000
19014.0000.0000.0000.0000.000
19016.0000.0000.0000.0000.000
19018.0000.0000.0000.0000.000
19020.0000.0000.0000.0000.000
19022.0000.0000.0000.0000.000
19024.0000.0000.0000.0000.000
19026.0000.0000.0000.0000.000
19028.0000.0000.0000.0000.000
19030.0000.0000.0000.0000.000
19032.0000.0000.0



You say you want the distance between two rings, but you only  
showed an index group for one of them (presumably), and the fact  
that you've gotten all zeroes as a result would suggest that you  
chose the same group twice for the distance calculation.  Which  
groups did you select?  Do they correspond to two, non-overlapping  
index groups?


-Justin




Quoting tekle...@ualberta.ca:


Dear Gromacs users,

I run my simulation for 20ns and want to extract  
aromatic-aromatic distance to see the stacking issue. But I am  
unable to get the value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
 123456789   10   11   12   13   14   15
16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
61   62
'''
'''
'''
''

[ RING ]
19   20   21   22   23   24   25   26   27   28   29   30
32   34   37   38   39   40   42   44

This is the ring I c

Re: [gmx-users] g_dist issue( Out put file)

[Justin A. Lemkul]

tekle...@ualberta.ca wrote:

Dear Justine,
Reading file PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr, VERSION 3.3.3 (single 
precision)

Group 0 (  System) has 28708 elements
Group 1 ( PAP) has   512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has20 elements
Select a group: 3
Selected 3: 'RING'
Select a group: 3
Selected 3: 'RING'
Reading frame   0 time 19000.000
Back Off! I just backed up DistPAP8HEP.xvg to ./#DistPAP8HEP.xvg.8#
Last frame500 time 2.000



which means I have to create two index file for two rings Ring_1 AND 
Ring_2 and choose both of them. If I am correct.




Yes.  Otherwise the distance from the center of mass of RING is calculated 
relative to the center of mass of RING, which by definition will always be zero.


-Justin


Rob




Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

The following is the out put.

# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 -o 
DistPAP8HEP.xvg

#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@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 "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.0000.0000.0000.000
19002.0000.0000.0000.0000.000
19004.0000.0000.0000.0000.000
19006.0000.0000.0000.0000.000
19008.0000.0000.0000.0000.000
19010.0000.0000.0000.0000.000
19012.0000.0000.0000.0000.000
19014.0000.0000.0000.0000.000
19016.0000.0000.0000.0000.000
19018.0000.0000.0000.0000.000
19020.0000.0000.0000.0000.000
19022.0000.0000.0000.0000.000
19024.0000.0000.0000.0000.000
19026.0000.0000.0000.0000.000
19028.0000.0000.0000.0000.000
19030.0000.0000.0000.0000.000
19032.0000.0000.0



You say you want the distance between two rings, but you only showed 
an index group for one of them (presumably), and the fact that you've 
gotten all zeroes as a result would suggest that you chose the same 
group twice for the distance calculation.  Which groups did you 
select?  Do they correspond to two, non-overlapping index groups?


-Justin




Quoting tekle...@ualberta.ca:


Dear Gromacs users,

I run my simulation for 20ns and want to extract aromatic-aromatic 
distance to see the stacking issue. But I am unable to get the value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
  123456789   10   11   12   13   
14   15
 16   17   18   19   20   21   22   23   24   25   26   27   28   
29   30
 31   32   33   34   35   36   37   38   39   40   41   42   43   
44   45
 46   47   48   49   50   51   52   53   54   55   56   57   58   
59   60

 61   62
 '''
 '''
 '''
 ''

[ RING ]
 19   20   21   22   23   24   25   26   27   28   29   30
 32   34   37   38   39   40   42   44

This is the ring I created plane in the index file.

I used this command line

g_dist -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 
-o DistPAP8HEP.xvg


but got the following like

I want to get the mean separation distance between two consecutive 
polyaromatic rings along the axis of stacking


can someone help.

rob



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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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http://lists.gromacs.org/mailman/listinfo/gmx-users
Pleas

Re: [gmx-users] g_dist issue( Out put file)

[teklebrh]

Dear Justine,
Reading file PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr, VERSION 3.3.3  
(single precision)

Group 0 (  System) has 28708 elements
Group 1 ( PAP) has   512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has20 elements
Select a group: 3
Selected 3: 'RING'
Select a group: 3
Selected 3: 'RING'
Reading frame   0 time 19000.000
Back Off! I just backed up DistPAP8HEP.xvg to ./#DistPAP8HEP.xvg.8#
Last frame500 time 2.000



which means I have to create two index file for two rings Ring_1 AND  
Ring_2 and choose both of them. If I am correct.


Rob




Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

The following is the out put.

# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2  
-o DistPAP8HEP.xvg

#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@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 "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.0000.0000.0000.000
19002.0000.0000.0000.0000.000
19004.0000.0000.0000.0000.000
19006.0000.0000.0000.0000.000
19008.0000.0000.0000.0000.000
19010.0000.0000.0000.0000.000
19012.0000.0000.0000.0000.000
19014.0000.0000.0000.0000.000
19016.0000.0000.0000.0000.000
19018.0000.0000.0000.0000.000
19020.0000.0000.0000.0000.000
19022.0000.0000.0000.0000.000
19024.0000.0000.0000.0000.000
19026.0000.0000.0000.0000.000
19028.0000.0000.0000.0000.000
19030.0000.0000.0000.0000.000
19032.0000.0000.0



You say you want the distance between two rings, but you only showed  
an index group for one of them (presumably), and the fact that  
you've gotten all zeroes as a result would suggest that you chose  
the same group twice for the distance calculation.  Which groups did  
you select?  Do they correspond to two, non-overlapping index groups?


-Justin




Quoting tekle...@ualberta.ca:


Dear Gromacs users,

I run my simulation for 20ns and want to extract aromatic-aromatic  
distance to see the stacking issue. But I am unable to get the  
value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
  123456789   10   11   12   13   14   15
 16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
 31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
 46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
 61   62
 '''
 '''
 '''
 ''

[ RING ]
 19   20   21   22   23   24   25   26   27   28   29   30
 32   34   37   38   39   40   42   44

This is the ring I created plane in the index file.

I used this command line

g_dist -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2  
-o DistPAP8HEP.xvg


but got the following like

I want to get the mean separation distance between two consecutive  
polyaromatic rings along the axis of stacking


can someone help.

rob



--
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--


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


--
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Re: [gmx-users] g_dist issue( Out put file)

[Justin A. Lemkul]

tekle...@ualberta.ca wrote:

The following is the out put.

# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 -o 
DistPAP8HEP.xvg

#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@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 "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.0000.0000.0000.000
19002.0000.0000.0000.0000.000
19004.0000.0000.0000.0000.000
19006.0000.0000.0000.0000.000
19008.0000.0000.0000.0000.000
19010.0000.0000.0000.0000.000
19012.0000.0000.0000.0000.000
19014.0000.0000.0000.0000.000
19016.0000.0000.0000.0000.000
19018.0000.0000.0000.0000.000
19020.0000.0000.0000.0000.000
19022.0000.0000.0000.0000.000
19024.0000.0000.0000.0000.000
19026.0000.0000.0000.0000.000
19028.0000.0000.0000.0000.000
19030.0000.0000.0000.0000.000
19032.0000.0000.0



You say you want the distance between two rings, but you only showed an index 
group for one of them (presumably), and the fact that you've gotten all zeroes 
as a result would suggest that you chose the same group twice for the distance 
calculation.  Which groups did you select?  Do they correspond to two, 
non-overlapping index groups?


-Justin




Quoting tekle...@ualberta.ca:


Dear Gromacs users,

I run my simulation for 20ns and want to extract aromatic-aromatic 
distance to see the stacking issue. But I am unable to get the value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
   123456789   10   11   12   13   
14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   
29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   
44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   
59   60

  61   62
  '''
  '''
  '''
  ''

[ RING ]
  19   20   21   22   23   24   25   26   27   28   29   30
  32   34   37   38   39   40   42   44

This is the ring I created plane in the index file.

I used this command line

g_dist -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 -o 
DistPAP8HEP.xvg


but got the following like

I want to get the mean separation distance between two consecutive 
polyaromatic rings along the axis of stacking


can someone help.

rob



--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before 
posting!
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--


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


--
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Re: [gmx-users] g_dist issue( Out put file)

[teklebrh]

The following is the out put.

# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 -o  
DistPAP8HEP.xvg

#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@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 "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.0000.0000.0000.000
19002.0000.0000.0000.0000.000
19004.0000.0000.0000.0000.000
19006.0000.0000.0000.0000.000
19008.0000.0000.0000.0000.000
19010.0000.0000.0000.0000.000
19012.0000.0000.0000.0000.000
19014.0000.0000.0000.0000.000
19016.0000.0000.0000.0000.000
19018.0000.0000.0000.0000.000
19020.0000.0000.0000.0000.000
19022.0000.0000.0000.0000.000
19024.0000.0000.0000.0000.000
19026.0000.0000.0000.0000.000
19028.0000.0000.0000.0000.000
19030.0000.0000.0000.0000.000
19032.0000.0000.0



Quoting tekle...@ualberta.ca:


Dear Gromacs users,

I run my simulation for 20ns and want to extract aromatic-aromatic  
distance to see the stacking issue. But I am unable to get the value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
   123456789   10   11   12   13   14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
  61   62
  '''
  '''
  '''
  ''

[ RING ]
  19   20   21   22   23   24   25   26   27   28   29   30
  32   34   37   38   39   40   42   44

This is the ring I created plane in the index file.

I used this command line

g_dist -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2  
-o DistPAP8HEP.xvg


but got the following like

I want to get the mean separation distance between two consecutive  
polyaromatic rings along the axis of stacking


can someone help.

rob



--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] g_dist issue

[teklebrh]

Dear Gromacs users,

I run my simulation for 20ns and want to extract aromatic-aromatic  
distance to see the stacking issue. But I am unable to get the value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
   123456789   10   11   12   13   14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
  61   62
  '''
  '''
  '''
  ''

[ RING ]
  19   20   21   22   23   24   25   26   27   28   29   30
  32   34   37   38   39   40   42   44

This is the ring I created plane in the index file.

I used this command line

g_dist -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 -o  
DistPAP8HEP.xvg


but got the following like

I want to get the mean separation distance between two consecutive  
polyaromatic rings along the axis of stacking


can someone help.

rob



--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] g_dist error?

[Justin A. Lemkul]

Marc Charendoff wrote:

Hello,

  I am in the middle of analyzing the distance between two atoms of 
a MD trajectory when I ran into the following error thus stopping at 3 
ns of a 4 ns trajectory. What could be the issue?


Select a group: 18
Selected 18: 'a_1899'
Select a group: 19
Selected 19: 'a_2498'
trn version: GMX_trn_file (double precision)
Reading frame   0 time0.000   
Back Off! I just backed up C4AHL_Y194.xvg to ./#C4AHL_Y194.xvg.1#
Reading frame3000 time 3000.000   
---

Program g_dist, VERSION 3.3.4
Source code file: trnio.c, line: 66

File input/output error:
Can not determine precision of trn file
---



Looks like your trajectory file is corrupted.  See what gmxcheck tells you, but 
it will likely come up with the same.  You may be able to parse out some usable 
frames with trjconv -b -e, but there may be a chunk of data missing as a result.


-Justin


Thanks, Marc



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 http://www.gromacs.org/search before posting!
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[gmx-users] g_dist error?

[Marc Charendoff]

Hello,

  I am in the middle of analyzing the distance between two atoms of a MD 
trajectory when I ran into the following error thus stopping at 3 ns of a 4 ns 
trajectory. What could be the issue?

Select a group: 18
Selected 18: 'a_1899'
Select a group: 19
Selected 19: 'a_2498'
trn version: GMX_trn_file (double precision)
Reading frame   0 time0.000   
Back Off! I just backed up C4AHL_Y194.xvg to ./#C4AHL_Y194.xvg.1#
Reading frame3000 time 3000.000   
---
Program g_dist, VERSION 3.3.4
Source code file: trnio.c, line: 66

File input/output error:
Can not determine precision of trn file
---

Thanks, Marc-- 
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Re: [gmx-users] g_dist and vsites

[Joe Joe]

I think I know the problem. I looked through gmx_dist and the distance is
calculated using the center of mass of the group. Since I am using Vsite the
mass of CB in ALA is set to zero. Is that correct?

Thanks,

Ilya


On Tue, Mar 9, 2010 at 11:44 AM, David van der Spoel
wrote:

> On 2010-03-09 20.01, Joe Joe wrote:
>
>> I also just tried on a different ALA and got the same problem.
>>
>
> can you please submit a bugzilla and upload files to reproduce the problem?
>
>
>> Ilya
>>
>>
>> On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe > > wrote:
>>
>>I am looking the the gmxdump output and everything seems consistent.
>>The only difference is that the numbering in the index file starts
>>at 1 whereas in the gmxdump the arrays are indexed starting at 0.
>>The coordinates look just fine.
>>
>>Thanks,
>>
>>Ilya
>>
>>
>>
>>On Tue, Mar 9, 2010 at 10:30 AM, Joe Joe >> wrote:
>>
>>I  trjconv/ed xtc to pdb and loaded into vmd. The coordinates
>>looked fine.
>>
>>I also
>>
>>tpbconv/ed topol.tpr to topol_subset.tpr.
>>
>>then I
>>
>>editconf/ed topol_subset.tpr to gro and looked at the
>>coordinates. Index file matched and structure looked whole in vmd.
>>
>>I will try the gmxdump
>>
>>Thanks,
>>
>>Ilya
>>
>>
>>
>>
>>On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel
>>mailto:sp...@xray.bmc.uu.se>> wrote:
>>
>>On 2010-03-09 19.16, Joe Joe wrote:
>>
>>yep.
>>
>>Have you gmxdump/ed the xtc to check the coordinates are right?
>>
>>
>>On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
>>mailto:sp...@xray.bmc.uu.se>
>>>>> wrote:
>>
>>On 2010-03-09 19.09, Joe Joe wrote:
>>
>>Hi I am trying to post process and xtc
>>trajectory using g_dist. I am
>>trying to calculate the CA-CB distance of an
>>Alanine residue but
>>I get
>>NAN in all the distance columns. It works for
>>the other residues
>>I've
>>tried (i.e. SER, VAL). I am using vsites in my
>>simulation and I
>>think it
>>may have some thing to do with the way gromacs
>>outputs the CB
>>positions
>>in the xtc file when the CB is part of the vsite
>>network. Any
>>thoughs?
>>
>>Thanks,
>>
>>Ilya
>>
>>Are you sure your index file matches the xtc/tpr?
>>
>>--
>>David van der Spoel, Ph.D., Professor of Biology
>>Dept. of Cell & Molec. Biol., Uppsala University.
>>Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>sp...@xray.bmc.uu.se 
>>> >>
>>
>>
>>http://folding.bmc.uu.se
>>--
>>gmx-users mailing list gmx-users@gromacs.org
>>
>>>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at
>>http://www.gromacs.org/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/mailing_lists/users.php
>>
>>
>>
>>
>>--
>>David van der Spoel, Ph.D., Professor of Biology
>>Dept. of Cell & Molec. Biol., Uppsala University.
>>Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>sp...@xray.bmc.uu.se 
>>http://folding.bmc.uu.se
>>--
>>gmx-users mailing list gmx-users@gromacs.org
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search
>>before posting!
>>Please don't post (un)subscribe requests to the list. Use
>>the www in

Re: [gmx-users] g_dist and vsites

[Joe Joe]

done, bug #402

On Tue, Mar 9, 2010 at 11:44 AM, David van der Spoel
wrote:

> On 2010-03-09 20.01, Joe Joe wrote:
>
>> I also just tried on a different ALA and got the same problem.
>>
>
> can you please submit a bugzilla and upload files to reproduce the problem?
>
>
>> Ilya
>>
>>
>> On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe > > wrote:
>>
>>I am looking the the gmxdump output and everything seems consistent.
>>The only difference is that the numbering in the index file starts
>>at 1 whereas in the gmxdump the arrays are indexed starting at 0.
>>The coordinates look just fine.
>>
>>Thanks,
>>
>>Ilya
>>
>>
>>
>>On Tue, Mar 9, 2010 at 10:30 AM, Joe Joe >> wrote:
>>
>>I  trjconv/ed xtc to pdb and loaded into vmd. The coordinates
>>looked fine.
>>
>>I also
>>
>>tpbconv/ed topol.tpr to topol_subset.tpr.
>>
>>then I
>>
>>editconf/ed topol_subset.tpr to gro and looked at the
>>coordinates. Index file matched and structure looked whole in vmd.
>>
>>I will try the gmxdump
>>
>>Thanks,
>>
>>Ilya
>>
>>
>>
>>
>>On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel
>>mailto:sp...@xray.bmc.uu.se>> wrote:
>>
>>On 2010-03-09 19.16, Joe Joe wrote:
>>
>>yep.
>>
>>Have you gmxdump/ed the xtc to check the coordinates are right?
>>
>>
>>On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
>>mailto:sp...@xray.bmc.uu.se>
>>>>> wrote:
>>
>>On 2010-03-09 19.09, Joe Joe wrote:
>>
>>Hi I am trying to post process and xtc
>>trajectory using g_dist. I am
>>trying to calculate the CA-CB distance of an
>>Alanine residue but
>>I get
>>NAN in all the distance columns. It works for
>>the other residues
>>I've
>>tried (i.e. SER, VAL). I am using vsites in my
>>simulation and I
>>think it
>>may have some thing to do with the way gromacs
>>outputs the CB
>>positions
>>in the xtc file when the CB is part of the vsite
>>network. Any
>>thoughs?
>>
>>Thanks,
>>
>>Ilya
>>
>>Are you sure your index file matches the xtc/tpr?
>>
>>--
>>David van der Spoel, Ph.D., Professor of Biology
>>Dept. of Cell & Molec. Biol., Uppsala University.
>>Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>sp...@xray.bmc.uu.se 
>>> >>
>>
>>
>>http://folding.bmc.uu.se
>>--
>>gmx-users mailing list gmx-users@gromacs.org
>>
>>>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at
>>http://www.gromacs.org/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/mailing_lists/users.php
>>
>>
>>
>>
>>--
>>David van der Spoel, Ph.D., Professor of Biology
>>Dept. of Cell & Molec. Biol., Uppsala University.
>>Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>sp...@xray.bmc.uu.se 
>>http://folding.bmc.uu.se
>>--
>>gmx-users mailing list gmx-users@gromacs.org
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>

Re: [gmx-users] g_dist and vsites

[David van der Spoel]

On 2010-03-09 20.01, Joe Joe wrote:

I also just tried on a different ALA and got the same problem.


can you please submit a bugzilla and upload files to reproduce the problem?



Ilya


On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe mailto:ilcho...@gmail.com>> wrote:

I am looking the the gmxdump output and everything seems consistent.
The only difference is that the numbering in the index file starts
at 1 whereas in the gmxdump the arrays are indexed starting at 0.
The coordinates look just fine.

Thanks,

Ilya



On Tue, Mar 9, 2010 at 10:30 AM, Joe Joe mailto:ilcho...@gmail.com>> wrote:

I  trjconv/ed xtc to pdb and loaded into vmd. The coordinates
looked fine.

I also

tpbconv/ed topol.tpr to topol_subset.tpr.

then I

editconf/ed topol_subset.tpr to gro and looked at the
coordinates. Index file matched and structure looked whole in vmd.

I will try the gmxdump

Thanks,

Ilya




On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel
mailto:sp...@xray.bmc.uu.se>> wrote:

On 2010-03-09 19.16, Joe Joe wrote:

yep.

Have you gmxdump/ed the xtc to check the coordinates are right?


On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
mailto:sp...@xray.bmc.uu.se>
>> wrote:

On 2010-03-09 19.09, Joe Joe wrote:

Hi I am trying to post process and xtc
trajectory using g_dist. I am
trying to calculate the CA-CB distance of an
Alanine residue but
I get
NAN in all the distance columns. It works for
the other residues
I've
tried (i.e. SER, VAL). I am using vsites in my
simulation and I
think it
may have some thing to do with the way gromacs
outputs the CB
positions
in the xtc file when the CB is part of the vsite
network. Any
thoughs?

Thanks,

Ilya

Are you sure your index file matches the xtc/tpr?

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se 
>

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Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] g_dist and vsites

[Joe Joe]

I also just tried on a different ALA and got the same problem.

Ilya


On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe  wrote:

> I am looking the the gmxdump output and everything seems consistent. The
> only difference is that the numbering in the index file starts at 1 whereas
> in the gmxdump the arrays are indexed starting at 0. The coordinates look
> just fine.
>
> Thanks,
>
> Ilya
>
>
>
> On Tue, Mar 9, 2010 at 10:30 AM, Joe Joe  wrote:
>
>> I  trjconv/ed xtc to pdb and loaded into vmd. The coordinates looked
>> fine.
>>
>> I also
>>
>> tpbconv/ed topol.tpr to topol_subset.tpr.
>>
>> then I
>>
>> editconf/ed topol_subset.tpr to gro and looked at the coordinates. Index
>> file matched and structure looked whole in vmd.
>>
>> I will try the gmxdump
>>
>> Thanks,
>>
>> Ilya
>>
>>
>>
>>
>> On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel <
>> sp...@xray.bmc.uu.se> wrote:
>>
>>> On 2010-03-09 19.16, Joe Joe wrote:
>>>
 yep.

>>> Have you gmxdump/ed the xtc to check the coordinates are right?
>>>

 On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
 mailto:sp...@xray.bmc.uu.se>> wrote:

On 2010-03-09 19.09, Joe Joe wrote:

Hi I am trying to post process and xtc trajectory using g_dist. I
 am
trying to calculate the CA-CB distance of an Alanine residue but
I get
NAN in all the distance columns. It works for the other residues
I've
tried (i.e. SER, VAL). I am using vsites in my simulation and I
think it
may have some thing to do with the way gromacs outputs the CB
positions
in the xtc file when the CB is part of the vsite network. Any
thoughs?

Thanks,

Ilya

Are you sure your index file matches the xtc/tpr?

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se 

http://folding.bmc.uu.se
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>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
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>>> interface or send it to gmx-users-requ...@gromacs.org.
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>>>
>>
>>
>
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Re: [gmx-users] g_dist and vsites

[Joe Joe]

I am looking the the gmxdump output and everything seems consistent. The
only difference is that the numbering in the index file starts at 1 whereas
in the gmxdump the arrays are indexed starting at 0. The coordinates look
just fine.

Thanks,

Ilya



On Tue, Mar 9, 2010 at 10:30 AM, Joe Joe  wrote:

> I  trjconv/ed xtc to pdb and loaded into vmd. The coordinates looked fine.
>
> I also
>
> tpbconv/ed topol.tpr to topol_subset.tpr.
>
> then I
>
> editconf/ed topol_subset.tpr to gro and looked at the coordinates. Index
> file matched and structure looked whole in vmd.
>
> I will try the gmxdump
>
> Thanks,
>
> Ilya
>
>
>
>
> On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel  > wrote:
>
>> On 2010-03-09 19.16, Joe Joe wrote:
>>
>>> yep.
>>>
>> Have you gmxdump/ed the xtc to check the coordinates are right?
>>
>>>
>>> On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
>>> mailto:sp...@xray.bmc.uu.se>> wrote:
>>>
>>>On 2010-03-09 19.09, Joe Joe wrote:
>>>
>>>Hi I am trying to post process and xtc trajectory using g_dist. I
>>> am
>>>trying to calculate the CA-CB distance of an Alanine residue but
>>>I get
>>>NAN in all the distance columns. It works for the other residues
>>>I've
>>>tried (i.e. SER, VAL). I am using vsites in my simulation and I
>>>think it
>>>may have some thing to do with the way gromacs outputs the CB
>>>positions
>>>in the xtc file when the CB is part of the vsite network. Any
>>>thoughs?
>>>
>>>Thanks,
>>>
>>>Ilya
>>>
>>>Are you sure your index file matches the xtc/tpr?
>>>
>>>--
>>>David van der Spoel, Ph.D., Professor of Biology
>>>Dept. of Cell & Molec. Biol., Uppsala University.
>>>Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>>sp...@xray.bmc.uu.se 
>>>
>>>http://folding.bmc.uu.se
>>>--
>>>gmx-users mailing list gmx-users@gromacs.org
>>>
>>>
>>>http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>posting!
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>>>interface or send it to gmx-users-requ...@gromacs.org
>>>.
>>>
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>>>
>>>
>>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
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Re: [gmx-users] g_dist and vsites

[Joe Joe]

I  trjconv/ed xtc to pdb and loaded into vmd. The coordinates looked fine.

I also

tpbconv/ed topol.tpr to topol_subset.tpr.

then I

editconf/ed topol_subset.tpr to gro and looked at the coordinates. Index
file matched and structure looked whole in vmd.

I will try the gmxdump

Thanks,

Ilya




On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel
wrote:

> On 2010-03-09 19.16, Joe Joe wrote:
>
>> yep.
>>
> Have you gmxdump/ed the xtc to check the coordinates are right?
>
>>
>> On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
>> mailto:sp...@xray.bmc.uu.se>> wrote:
>>
>>On 2010-03-09 19.09, Joe Joe wrote:
>>
>>Hi I am trying to post process and xtc trajectory using g_dist. I
>> am
>>trying to calculate the CA-CB distance of an Alanine residue but
>>I get
>>NAN in all the distance columns. It works for the other residues
>>I've
>>tried (i.e. SER, VAL). I am using vsites in my simulation and I
>>think it
>>may have some thing to do with the way gromacs outputs the CB
>>positions
>>in the xtc file when the CB is part of the vsite network. Any
>>thoughs?
>>
>>Thanks,
>>
>>Ilya
>>
>>Are you sure your index file matches the xtc/tpr?
>>
>>--
>>David van der Spoel, Ph.D., Professor of Biology
>>Dept. of Cell & Molec. Biol., Uppsala University.
>>Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>sp...@xray.bmc.uu.se 
>>
>>http://folding.bmc.uu.se
>>--
>>gmx-users mailing list gmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
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Re: [gmx-users] g_dist and vsites

[David van der Spoel]

On 2010-03-09 19.16, Joe Joe wrote:

yep.

Have you gmxdump/ed the xtc to check the coordinates are right?


On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
mailto:sp...@xray.bmc.uu.se>> wrote:

On 2010-03-09 19.09, Joe Joe wrote:

Hi I am trying to post process and xtc trajectory using g_dist. I am
trying to calculate the CA-CB distance of an Alanine residue but
I get
NAN in all the distance columns. It works for the other residues
I've
tried (i.e. SER, VAL). I am using vsites in my simulation and I
think it
may have some thing to do with the way gromacs outputs the CB
positions
in the xtc file when the CB is part of the vsite network. Any
thoughs?

Thanks,

Ilya

Are you sure your index file matches the xtc/tpr?

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se 
http://folding.bmc.uu.se
--
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] g_dist and vsites

[Joe Joe]

Hi I am trying to post process and xtc trajectory using g_dist. I am trying
to calculate the CA-CB distance of an Alanine residue but I get NAN in all
the distance columns. It works for the other residues I've tried (i.e. SER,
VAL). I am using vsites in my simulation and I think it may have some thing
to do with the way gromacs outputs the CB positions in the xtc file when the
CB is part of the vsite network. Any thoughs?

Thanks,

Ilya
-- 
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Re: [gmx-users] g_dist and vsites

[Joe Joe]

yep.

On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
wrote:

> On 2010-03-09 19.09, Joe Joe wrote:
>
>> Hi I am trying to post process and xtc trajectory using g_dist. I am
>> trying to calculate the CA-CB distance of an Alanine residue but I get
>> NAN in all the distance columns. It works for the other residues I've
>> tried (i.e. SER, VAL). I am using vsites in my simulation and I think it
>> may have some thing to do with the way gromacs outputs the CB positions
>> in the xtc file when the CB is part of the vsite network. Any thoughs?
>>
>> Thanks,
>>
>> Ilya
>>
>>  Are you sure your index file matches the xtc/tpr?
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] g_dist and vsites

[David van der Spoel]

On 2010-03-09 19.09, Joe Joe wrote:

Hi I am trying to post process and xtc trajectory using g_dist. I am
trying to calculate the CA-CB distance of an Alanine residue but I get
NAN in all the distance columns. It works for the other residues I've
tried (i.e. SER, VAL). I am using vsites in my simulation and I think it
may have some thing to do with the way gromacs outputs the CB positions
in the xtc file when the CB is part of the vsite network. Any thoughs?

Thanks,

Ilya


Are you sure your index file matches the xtc/tpr?

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] g_dist and vsites

[Joe Joe]

Hi I am trying to post process and xtc trajectory using g_dist. I am trying
to calculate the CA-CB distance of an Alanine residue but I get NAN in all
the distance columns. It works for the other residues I've tried (i.e. SER,
VAL). I am using vsites in my simulation and I think it may have some thing
to do with the way gromacs outputs the CB positions in the xtc file when the
CB is part of the vsite network. Any thoughs?

Thanks,

Ilya
-- 
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Re: [gmx-users] g_dist output

[John Shultz]

I tried using the xtc instead but it says the atom range is outside the index


g_dist -f md.xtc -s md.tpr -n index.ndx < protein_lig.txt
 :-)  G  R  O  M  A  C  S  (-:

 Gallium Rubidium Oxygen Manganese Argon Carbon Silicon

:-)  VERSION 4.0.5  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

:-)  g_dist  (-:

Option Filename  Type Description

  -f md.xtc  InputTrajectory: xtc trr trj gro g96 pdb cpt
  -s md.tpr  InputRun input file: tpr tpb tpa
  -n  index.ndx  Input, Opt!  Index file
  -o   dist.xvg  Output, Opt. xvgr/xmgr file
 -lt   lifetime.xvg  Output, Opt. xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint19  Set the nicelevel
-b   time   0   First frame (ps) to read from trajectory
-e   time   0   Last frame (ps) to read from trajectory
-dt  time   0   Only use frame when t MOD dt = first time (ps)
-[no]xvgrbool   yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-distreal   0   Print all atoms in group 2 closer than dist to
the center of mass of group 1

Reading file md.tpr, VERSION 4.0.5 (single precision)
Group 0 (  System) has 38210 elements
Group 1 ( Protein) has  3868 elements
Group 2 (   Protein-H) has  1980 elements
Group 3 ( C-alpha) has   244 elements
Group 4 (Backbone) has   732 elements
Group 5 (   MainChain) has   974 elements
Group 6 (MainChain+Cb) has  1206 elements
Group 7 ( MainChain+H) has  1198 elements
Group 8 (   SideChain) has  2670 elements
Group 9 ( SideChain-H) has  1006 elements
Group10 ( Prot-Masses) has  3868 elements
Group11 ( Non-Protein) has 34342 elements
Group12 ( LIG) has46 elements
Group13 ( SOL) has 34212 elements
Group14 (  Na) has48 elements
Group15 (  Cl) has36 elements
Group16 (   Other) has 34342 elements
Select a group: Selected 1: 'Protein'
Select a group: Selected 12: 'LIG'
Reading frame   0 time0.000
---
Program g_dist, VERSION 4.0.5
Source code file: gmx_dist.c, line: 165

Fatal error:
Atom number 3914 in an index group is larger than number of atoms in
the trajectory (3868)

---

"Shaken, not Stirred" (J. Bond)


On Tue, Mar 9, 2010 at 9:03 AM, John Shultz  wrote:
> Here is what our script is doing. It looks to me like we are analyzing
> the tpr when we should be checking the xtc or trr if I understand you
> correctly. And if we look at the trajectory we can measure the drift
> for the entire simulation rather than a specific instance.
>
>
> make_ndx -f md.tpr < make_ndx.txt
>                         :-)  G  R  O  M  A  C  S  (-:
>
>                      GROup of MAchos and Cynical Suckers
>
>                            :-)  VERSION 4.0.5  (-:
>
>
>      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>             Copyright (c) 2001-2008, The GROMACS development team,
>            check out http://www.gromacs.org for more information.
>
>         This program is free software; you can redistribute it and/or
>          modify it under the terms of the GNU General Public License
>         as published by the Free Software Foundation; either version 2
>             of the License, or (at your option) any later version.
>
>                               :-)  make_ndx  (-:
>
> Option     Filename  Type         Description
> 
>  -f         md.tpr  Input, Opt!  Structure file: gro g96 pdb tpr tpb tpa
>  -n      index.ndx  Input, Opt., Mult. Index file
>  -o      index.ndx  Output       Index file
>
> Option       Type   Value   Description
> --
> -[no]h       bool   no      Print help info and quit
> -nice        int    0       Set the nicelevel
> -natoms      int    0       set number of atoms (default: read from

Re: [gmx-users] g_dist output

[Justin A. Lemkul]

John Shultz wrote:

Here is what our script is doing. It looks to me like we are analyzing
the tpr when we should be checking the xtc or trr if I understand you
correctly. And if we look at the trajectory we can measure the drift
for the entire simulation rather than a specific instance.


The .tpr file is required input for g_dist, but the frame(s) actually analyzed 
are in the generic trajectory file passed to the -f flag.  Both the .tpr and 
trajectory are required input.  This trajectory can be .xtc, .trr, .gro, .pdb, 
or a few others.  The program uses information about the atoms in the .tpr file 
to carry out the analysis on the trajectory.  As you've shown, you pass "md.gro" 
to g_dist, so you will only ever have that .gro file's information.  While it is 
possible to write the entire trajectory in .gro format, this is very 
inconvenient, since the file size gets large in a hurry, so I assume your 
"md.gro" is just a single frame, so you're getting exactly what you should 
expect.  If you want distances over time, pass a .xtc or .trr to the -f option 
of g_dist.


-Justin




make_ndx -f md.tpr < make_ndx.txt
 :-)  G  R  O  M  A  C  S  (-:

  GROup of MAchos and Cynical Suckers

:-)  VERSION 4.0.5  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

   :-)  make_ndx  (-:

Option Filename  Type Description

  -f md.tpr  Input, Opt!  Structure file: gro g96 pdb tpr tpb tpa
  -n  index.ndx  Input, Opt., Mult. Index file
  -o  index.ndx  Output   Index file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint0   Set the nicelevel
-natoms  int0   set number of atoms (default: read from
coordinate or index file)

Reading file md.tpr, VERSION 4.0.5 (single precision)

Reading structure file
Reading file md.tpr, VERSION 4.0.5 (single precision)
Going to read 0 old index file(s)
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are: 11489  OTHER residues
There are:   244PROTEIN residues
There are: 0DNA residues
Analysing Protein...
Analysing Other...

  0 System  : 38210 atoms
  1 Protein :  3868 atoms
  2 Protein-H   :  1980 atoms
  3 C-alpha :   244 atoms
  4 Backbone:   732 atoms
  5 MainChain   :   974 atoms
  6 MainChain+Cb:  1206 atoms
  7 MainChain+H :  1198 atoms
  8 SideChain   :  2670 atoms
  9 SideChain-H :  1006 atoms
 10 Prot-Masses :  3868 atoms
 11 Non-Protein : 34342 atoms
 12 LIG :46 atoms
 13 SOL : 34212 atoms
 14 Na  :48 atoms
 15 Cl  :36 atoms
 16 Other   : 34342 atoms

 nr : group   !   'name' nr name   'splitch' nrEnter: list groups
 'a': atom&   'del' nr 'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr'splitat' nr'h': help
 'r': residue 'res' nr 'chain' char
 "name": group'case': case sensitive   'q': save and quit

Copied index group 0 'System'

Syntax error: "q "

gcq#89: "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)

g_dist -f md.gro -s md.tpr -n index.ndx < protein_lig.txt
 :-)  G  R  O  M  A  C  S  (-:

  GROup of MAchos and Cynical Suckers

:-)  VERSION 4.0.5  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

:-)  g_dist  (-:

Option Filename  Type Description

  -f 

[gmx-users] g_dist output

[John Shultz]

Hello,

I am seeking clarification on what this output means. I believe it
says that the x axis is divided into 4 time intervals and they are
plotted against a y axis that measures total distance along all 3
dimensional coordinates.
Am I reading this correctly?

# This file was created Sat Jan 30 00:20:03 2010
# by the following command:
# g_dist -f md.gro -s md.tpr -n index.ndx
#
# g_dist is part of G R O M A C S:
#
# Glycine aRginine prOline Methionine Alanine Cystine Serine
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@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 "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
   0.0000.06194480.05833030.0099401   -0.0183282




-- 
Jack
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Re: [gmx-users] g_dist output

[Justin A. Lemkul]

John Shultz wrote:

I tried using the xtc instead but it says the atom range is outside the index



Well, 3868 is the number of atoms in your protein, so I'm guessing you set 
"xtc_grps = Protein" in the .mdp file.  If you want to analyze other groups, 
then you have to actually save their coordinates when running your MD.


-Justin



g_dist -f md.xtc -s md.tpr -n index.ndx < protein_lig.txt
 :-)  G  R  O  M  A  C  S  (-:

 Gallium Rubidium Oxygen Manganese Argon Carbon Silicon

:-)  VERSION 4.0.5  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

:-)  g_dist  (-:

Option Filename  Type Description

  -f md.xtc  InputTrajectory: xtc trr trj gro g96 pdb cpt
  -s md.tpr  InputRun input file: tpr tpb tpa
  -n  index.ndx  Input, Opt!  Index file
  -o   dist.xvg  Output, Opt. xvgr/xmgr file
 -lt   lifetime.xvg  Output, Opt. xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint19  Set the nicelevel
-b   time   0   First frame (ps) to read from trajectory
-e   time   0   Last frame (ps) to read from trajectory
-dt  time   0   Only use frame when t MOD dt = first time (ps)
-[no]xvgrbool   yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-distreal   0   Print all atoms in group 2 closer than dist to
the center of mass of group 1

Reading file md.tpr, VERSION 4.0.5 (single precision)
Group 0 (  System) has 38210 elements
Group 1 ( Protein) has  3868 elements
Group 2 (   Protein-H) has  1980 elements
Group 3 ( C-alpha) has   244 elements
Group 4 (Backbone) has   732 elements
Group 5 (   MainChain) has   974 elements
Group 6 (MainChain+Cb) has  1206 elements
Group 7 ( MainChain+H) has  1198 elements
Group 8 (   SideChain) has  2670 elements
Group 9 ( SideChain-H) has  1006 elements
Group10 ( Prot-Masses) has  3868 elements
Group11 ( Non-Protein) has 34342 elements
Group12 ( LIG) has46 elements
Group13 ( SOL) has 34212 elements
Group14 (  Na) has48 elements
Group15 (  Cl) has36 elements
Group16 (   Other) has 34342 elements
Select a group: Selected 1: 'Protein'
Select a group: Selected 12: 'LIG'
Reading frame   0 time0.000
---
Program g_dist, VERSION 4.0.5
Source code file: gmx_dist.c, line: 165

Fatal error:
Atom number 3914 in an index group is larger than number of atoms in
the trajectory (3868)

---

"Shaken, not Stirred" (J. Bond)


On Tue, Mar 9, 2010 at 9:03 AM, John Shultz  wrote:

Here is what our script is doing. It looks to me like we are analyzing
the tpr when we should be checking the xtc or trr if I understand you
correctly. And if we look at the trajectory we can measure the drift
for the entire simulation rather than a specific instance.


make_ndx -f md.tpr < make_ndx.txt
:-)  G  R  O  M  A  C  S  (-:

 GROup of MAchos and Cynical Suckers

   :-)  VERSION 4.0.5  (-:


 Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
   check out http://www.gromacs.org for more information.

This program is free software; you can redistribute it and/or
 modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

  :-)  make_ndx  (-:

Option Filename  Type Description

 -f md.tpr  Input, Opt!  Structure file: gro g96 pdb tpr tpb tpa
 -n  index.ndx  Input, Opt., Mult. Index file
 -o  index.ndx  Output   Index file

Option   Type   Value   Description
--

Re: [gmx-users] g_dist output

[John Shultz]

Thank you Justin. The LIG was missing from our default mdp parameters.
That explains why we could not use the xtc file. I am adding it now.

On Tue, Mar 9, 2010 at 9:11 AM, Justin A. Lemkul  wrote:
>
>
> John Shultz wrote:
>>
>> I tried using the xtc instead but it says the atom range is outside the
>> index
>>
>
> Well, 3868 is the number of atoms in your protein, so I'm guessing you set
> "xtc_grps = Protein" in the .mdp file.  If you want to analyze other groups,
> then you have to actually save their coordinates when running your MD.
>
> -Justin
>
>>
>> g_dist -f md.xtc -s md.tpr -n index.ndx < protein_lig.txt
>>                         :-)  G  R  O  M  A  C  S  (-:
>>
>>             Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
>>
>>                            :-)  VERSION 4.0.5  (-:
>>
>>
>>      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>>       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>             Copyright (c) 2001-2008, The GROMACS development team,
>>            check out http://www.gromacs.org for more information.
>>
>>         This program is free software; you can redistribute it and/or
>>          modify it under the terms of the GNU General Public License
>>         as published by the Free Software Foundation; either version 2
>>             of the License, or (at your option) any later version.
>>
>>                                :-)  g_dist  (-:
>>
>> Option     Filename  Type         Description
>> 
>>  -f         md.xtc  Input        Trajectory: xtc trr trj gro g96 pdb cpt
>>  -s         md.tpr  Input        Run input file: tpr tpb tpa
>>  -n      index.ndx  Input, Opt!  Index file
>>  -o       dist.xvg  Output, Opt. xvgr/xmgr file
>>  -lt   lifetime.xvg  Output, Opt. xvgr/xmgr file
>>
>> Option       Type   Value   Description
>> --
>> -[no]h       bool   no      Print help info and quit
>> -nice        int    19      Set the nicelevel
>> -b           time   0       First frame (ps) to read from trajectory
>> -e           time   0       Last frame (ps) to read from trajectory
>> -dt          time   0       Only use frame when t MOD dt = first time (ps)
>> -[no]xvgr    bool   yes     Add specific codes (legends etc.) in the
>> output
>>                            xvg files for the xmgrace program
>> -dist        real   0       Print all atoms in group 2 closer than dist to
>>                            the center of mass of group 1
>>
>> Reading file md.tpr, VERSION 4.0.5 (single precision)
>> Group     0 (      System) has 38210 elements
>> Group     1 (     Protein) has  3868 elements
>> Group     2 (   Protein-H) has  1980 elements
>> Group     3 (     C-alpha) has   244 elements
>> Group     4 (    Backbone) has   732 elements
>> Group     5 (   MainChain) has   974 elements
>> Group     6 (MainChain+Cb) has  1206 elements
>> Group     7 ( MainChain+H) has  1198 elements
>> Group     8 (   SideChain) has  2670 elements
>> Group     9 ( SideChain-H) has  1006 elements
>> Group    10 ( Prot-Masses) has  3868 elements
>> Group    11 ( Non-Protein) has 34342 elements
>> Group    12 (         LIG) has    46 elements
>> Group    13 (         SOL) has 34212 elements
>> Group    14 (          Na) has    48 elements
>> Group    15 (          Cl) has    36 elements
>> Group    16 (       Other) has 34342 elements
>> Select a group: Selected 1: 'Protein'
>> Select a group: Selected 12: 'LIG'
>> Reading frame       0 time    0.000
>> ---
>> Program g_dist, VERSION 4.0.5
>> Source code file: gmx_dist.c, line: 165
>>
>> Fatal error:
>> Atom number 3914 in an index group is larger than number of atoms in
>> the trajectory (3868)
>>
>> ---
>>
>> "Shaken, not Stirred" (J. Bond)
>>
>>
>> On Tue, Mar 9, 2010 at 9:03 AM, John Shultz 
>> wrote:
>>>
>>> Here is what our script is doing. It looks to me like we are analyzing
>>> the tpr when we should be checking the xtc or trr if I understand you
>>> correctly. And if we look at the trajectory we can measure the drift
>>> for the entire simulation rather than a specific instance.
>>>
>>>
>>> make_ndx -f md.tpr < make_ndx.txt
>>>                        :-)  G  R  O  M  A  C  S  (-:
>>>
>>>                     GROup of MAchos and Cynical Suckers
>>>
>>>                           :-)  VERSION 4.0.5  (-:
>>>
>>>
>>>     Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>>>      Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>>            Copyright (c) 2001-2008, The GROMACS development team,
>>>           check out http://www.gromacs.org for more information.
>>>
>>>        This program is free software; you can redistribute it and/or
>>>         modify it under the terms of the GNU General Public License
>>>        as published by the Free S

Re: [gmx-users] g_dist output

[Justin A. Lemkul]

John Shultz wrote:

How come time is always  0.000



You're analyzing a .gro file, so there is no time information stored.  If you 
analyze a trajectory (i.e., .xtc or .trr), then the time is saved in the 
individual frames.


-Justin


On Tue, Mar 9, 2010 at 8:16 AM, Justin A. Lemkul  wrote:


John Shultz wrote:

Hello,

I am seeking clarification on what this output means. I believe it
says that the x axis is divided into 4 time intervals and they are
plotted against a y axis that measures total distance along all 3
dimensional coordinates.
Am I reading this correctly?


There should be no decomposition of time intervals here.  Distance is
plotted continuously as a function of time.  The first column is time, then
the total distance, then each of the x, y, and z components of that
distance.

-Justin


# This file was created Sat Jan 30 00:20:03 2010
# by the following command:
# g_dist -f md.gro -s md.tpr -n index.ndx
#
# g_dist is part of G R O M A C S:
#
# Glycine aRginine prOline Methionine Alanine Cystine Serine
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@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 "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
  0.0000.06194480.05833030.0099401   -0.0183282





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
Please search the archive at http://www.gromacs.org/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.
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
Please search the archive at http://www.gromacs.org/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.

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