Re: [gmx-users] g_rms alignment question

[Justin Lemkul]

On 12/4/12 3:10 AM, Tsjerk Wassenaar wrote:

Hi Jia,

You can use trjconv for custom fitting, and then feed the fitted trajectory
to g_rms, not using fitting there. Either that's using -nofit or -fit none.



The same can be done in one step by using an index file with g_rms and choosing 
that group for fitting.


-Justin


Cheers,

Tsjerk


On Tue, Dec 4, 2012 at 6:06 AM, Jia Xu  wrote:


Dear gromacs users,
 I have a trajectory of 500-atom system and would like to obtain RMSD of
all atoms but only aligned to residue 1-400 of a reference structure. Is
there any way to do this?
 Thank you so much!
Regards,
Jia
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Re: [gmx-users] g_rms alignment question

[Tsjerk Wassenaar]

Hi Jia,

You can use trjconv for custom fitting, and then feed the fitted trajectory
to g_rms, not using fitting there. Either that's using -nofit or -fit none.

Cheers,

Tsjerk


On Tue, Dec 4, 2012 at 6:06 AM, Jia Xu  wrote:

> Dear gromacs users,
> I have a trajectory of 500-atom system and would like to obtain RMSD of
> all atoms but only aligned to residue 1-400 of a reference structure. Is
> there any way to do this?
> Thank you so much!
> Regards,
> Jia
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Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
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[gmx-users] g_rms alignment question

[Jia Xu]

Dear gromacs users,
I have a trajectory of 500-atom system and would like to obtain RMSD of
all atoms but only aligned to residue 1-400 of a reference structure. Is
there any way to do this?
Thank you so much!
Regards,
Jia
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Re: [gmx-users] g_rms/rmsf: fit vs. nofit

[Justin Lemkul]

On 11/2/12 7:11 PM, Peter C. Lai wrote:

Hi

I have sort of a noob question about when to fit and when not to fit when
computing rmsd and rmsf.

My use-case is to look at the motion of different domains of a protein
where there are atoms near the COM of the starting structure that remain
relatively stable throughout the simulation according to g_traj.

Right now, I have been using trjconv -center the trajectory on this core alpha
carbon then using trjconv -dump and grompp to generate a recentered starting
structure .tpr. Then I am running g_rms or g_rmsf -nofit against the recentered
.tpr as the reference.

Is this wildly inappropriate? Should I be fitting against an index group
consisting of that atom instead? Because the backbone is supposed to be
shifting I want to minimize any artifacts that would potentially dampen an
observable residue motion just because the rmsd was computed after a fit,
and centering the trajectory on an atom near the starting COM would minimize
distances traveled due to COM diffusion through the solvent.



Centering on a single atom can give you spurious results - you'll get false 
contributions from global rotation.  You also can't fit to a single atom, so you 
need a group to which to fit.  If you're looking at motions of one domain 
relative to another, you could fit to one domain and measure relative to it, 
since then the other domain is free to move with respect to the fitted domain.


-Justin

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Department of Biochemistry
Virginia Tech
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[gmx-users] g_rms/rmsf: fit vs. nofit

[Peter C. Lai]

Hi

I have sort of a noob question about when to fit and when not to fit when 
computing rmsd and rmsf.

My use-case is to look at the motion of different domains of a protein
where there are atoms near the COM of the starting structure that remain 
relatively stable throughout the simulation according to g_traj. 

Right now, I have been using trjconv -center the trajectory on this core alpha
carbon then using trjconv -dump and grompp to generate a recentered starting
structure .tpr. Then I am running g_rms or g_rmsf -nofit against the recentered
.tpr as the reference.

Is this wildly inappropriate? Should I be fitting against an index group
consisting of that atom instead? Because the backbone is supposed to be 
shifting I want to minimize any artifacts that would potentially dampen an 
observable residue motion just because the rmsd was computed after a fit,
and centering the trajectory on an atom near the starting COM would minimize
distances traveled due to COM diffusion through the solvent.

-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics Div. of Research   | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
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Re: [gmx-users] g_rms problem

[Albert]

On 10/28/2012 05:52 PM, Christopher Neale wrote:

I thought you said that you have 1000 structures. It seems like you only have 
6? Nevertheless, I am glad that trjcat worked for you.

I don't know what is going on with your RMSD values, but I suggest that you 
start a separate post with a new subject line for that. I suspect that you need 
to do some fitting.

Chris.


thank you for kind reply. I just use 6 for testing.
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[gmx-users] g_rms problem

[Christopher Neale]

I thought you said that you have 1000 structures. It seems like you only have 
6? Nevertheless, I am glad that trjcat worked for you.

I don't know what is going on with your RMSD values, but I suggest that you 
start a separate post with a new subject line for that. I suspect that you need 
to do some fitting.

Chris.

-- original message --

thanks a lot for kind reply.
The outout for

for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |head

is:
1838
1838
1838
1838
1838
1838

The output for

for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |tail

is also:
1838
1838
1838
1838
1838
1838


It seems that trjcat works fine, although the time is 0 for all frames. 
Here is the command I use:

trjcat -cat -keeplast -f *.pdb -o out.xtc

g_rms -f out.xtc -s 001.pdb -o rmsd.xvg

However, I find a problem with the results. Since most part of each PDB 
file overlapped very well only a small loop is different. I first 
calculate the rmsd of backbone and got:

@ subtitle "Backbone after lsq fit to Backbone"
0.0000.003
0.0000.3306260
0.0000.2545602
0.0000.3293277
0.0000.2299789
0.0000.3216407

Then I calculate the loop region and got:

@ subtitle "Backbone_&_r_120-131 after lsq fit to Backbone"
0.0000.003
0.0000.1526730
0.0000.1202507
0.0000.1449232
0.0000.1318949
0.0000.1675032

As we can see, the rmsd of loop region is smaller than the backbone 
which I think it should be reversed...

thank you very much.

On 10/28/2012 05:03 PM, Christopher Neale wrote:
> First, please let me complain that you did not run those 2 commands and post 
> the full output with the line on which you entered the command (for each 
> one). Each command is expected to give you 10 lines of output, but you posted 
> a single group of 12 lines. That seems like unlikely output and just confuses 
> things.
>
> Second, I am not sure that you can simply cat the results of rosetta together 
> (or any pdb files). I suggest that you try using trjcat -cat -keeplast to put 
> them together or convert them all to .gro files with a loop over editconf and 
> then join them with cat (or trjcat).
>
> Chris.
>
>
>> How many atoms are in each .pdb file?
>>
>> for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |head
>> for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |tail
>>
>> Chris.
> Hi Chris:
>
>they are 1838 atoms in each PDB file and all of them are full atoms. I
> run the command you provide and I got:
>
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
>
> When I try to reuse g_rms, the problem is still the same.
>
> thank you very much
>

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Re: [gmx-users] g_rms problem

[Albert]

hello Chris:

thanks a lot for kind reply.
The outout for

for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |head

is:
1838
1838
1838
1838
1838
1838

The output for

for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |tail

is also:
1838
1838
1838
1838
1838
1838


It seems that trjcat works fine, although the time is 0 for all frames. 
Here is the command I use:


trjcat -cat -keeplast -f *.pdb -o out.xtc

g_rms -f out.xtc -s 001.pdb -o rmsd.xvg

However, I find a problem with the results. Since most part of each PDB 
file overlapped very well only a small loop is different. I first 
calculate the rmsd of backbone and got:


@ subtitle "Backbone after lsq fit to Backbone"
   0.0000.003
   0.0000.3306260
   0.0000.2545602
   0.0000.3293277
   0.0000.2299789
   0.0000.3216407

Then I calculate the loop region and got:

@ subtitle "Backbone_&_r_120-131 after lsq fit to Backbone"
   0.0000.003
   0.0000.1526730
   0.0000.1202507
   0.0000.1449232
   0.0000.1318949
   0.0000.1675032

As we can see, the rmsd of loop region is smaller than the backbone 
which I think it should be reversed...


thank you very much.

On 10/28/2012 05:03 PM, Christopher Neale wrote:

First, please let me complain that you did not run those 2 commands and post 
the full output with the line on which you entered the command (for each one). 
Each command is expected to give you 10 lines of output, but you posted a 
single group of 12 lines. That seems like unlikely output and just confuses 
things.

Second, I am not sure that you can simply cat the results of rosetta together 
(or any pdb files). I suggest that you try using trjcat -cat -keeplast to put 
them together or convert them all to .gro files with a loop over editconf and 
then join them with cat (or trjcat).

Chris.



How many atoms are in each .pdb file?

for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |head
for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |tail

Chris.

Hi Chris:

   they are 1838 atoms in each PDB file and all of them are full atoms. I
run the command you provide and I got:

1838
1838
1838
1838
1838
1838
1838
1838
1838
1838
1838
1838

When I try to reuse g_rms, the problem is still the same.

thank you very much



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[gmx-users] g_rms problem

[Christopher Neale]

First, please let me complain that you did not run those 2 commands and post 
the full output with the line on which you entered the command (for each one). 
Each command is expected to give you 10 lines of output, but you posted a 
single group of 12 lines. That seems like unlikely output and just confuses 
things.

Second, I am not sure that you can simply cat the results of rosetta together 
(or any pdb files). I suggest that you try using trjcat -cat -keeplast to put 
them together or convert them all to .gro files with a loop over editconf and 
then join them with cat (or trjcat).

Chris.


> How many atoms are in each .pdb file?
>
> for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |head
> for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |tail
>
> Chris.

Hi Chris:

  they are 1838 atoms in each PDB file and all of them are full atoms. I 
run the command you provide and I got:

1838
1838
1838
1838
1838
1838
1838
1838
1838
1838
1838
1838

When I try to reuse g_rms, the problem is still the same.

thank you very much

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Re: [gmx-users] g_rms problem

[Albert]

On 10/28/2012 01:19 PM, Christopher Neale wrote:

How many atoms are in each .pdb file?

for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |head
for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |tail

Chris.


Hi Chris:

 they are 1838 atoms in each PDB file and all of them are full atoms. I 
run the command you provide and I got:


1838
1838
1838
1838
1838
1838
1838
1838
1838
1838
1838
1838

When I try to reuse g_rms, the problem is still the same.

thank you very much

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[gmx-users] g_rms problem

[Christopher Neale]

How many atoms are in each .pdb file?

for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |head
for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |tail

Chris.

-- original message --

   I've 1000 separate pdb files generated by other Rosetta and I would 
like to calculate the RMSD between them. I use command:

cat *.pdb > all
mv all all.pdb

to merge it.

then I use g_rms to calculate the rmsd between them:

g_rms -f all.pdb -s 0001.pdb -o rmsd.xvg

However, g_rms only give one rmsd value for it with following messages:
warnings: if there are broken molecules in the trjectory file,  they can 
not be made whole without a run input file

reading frame  0 time -1.
Warning: topology has 1840 atoms, whereas trjectory has 7360 '',. 7360 atoms


I am just wondering how can I make g_rms works fine correctly?

thank you very much
Albert

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[gmx-users] g_rms problem

[Albert]

hello:

  I've 1000 separate pdb files generated by other Rosetta and I would 
like to calculate the RMSD between them. I use command:


cat *.pdb > all
mv all all.pdb

to merge it.

then I use g_rms to calculate the rmsd between them:

g_rms -f all.pdb -s 0001.pdb -o rmsd.xvg

However, g_rms only give one rmsd value for it with following messages:
warnings: if there are broken molecules in the trjectory file,  they can 
not be made whole without a run input file


reading frame  0 time -1.
Warning: topology has 1840 atoms, whereas trjectory has 7360 '',. 7360 atoms


I am just wondering how can I make g_rms works fine correctly?

thank you very much
Albert
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Re: [gmx-users] g_rms and g_rmsdist on initial structure

[Erik Marklund]

Hi,

Since gromos-forcefields are not strictly all-atom forcefields, there might be 
a mismatch between atoms in the two structures.

Best,

Erik

24 aug 2012 kl. 15.35 skrev Hsin-Lin Chiang:

> Hi,
> 
> For example, I have a A.pdb as a initial structure file.
> And I just used pdb2gmx on it to generate another B.pdb file with GROMOS96 
> 43a1 as its force filed.
> Then I select C-alpha atoms to calculate RMSD.
> echo 3 | g_rms -f B.pdb -s A.pdb
> I suppose the RMSD value should be 0, but the value is high to about 0.5nm.
> Can someone explain for me?
> 
> Sincerely yours,
> Hsin-Lin
> 
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[gmx-users] g_rms and g_rmsdist on initial structure

[Hsin-Lin Chiang]

Hi,

For example, I have a A.pdb as a initial structure file.
And I just used pdb2gmx on it to generate another B.pdb file with 
GROMOS96 43a1 as its force filed.

Then I select C-alpha atoms to calculate RMSD.
echo 3 | g_rms -f B.pdb -s A.pdb
I suppose the RMSD value should be 0, but the value is high to about 0.5nm.
Can someone explain for me?

Sincerely yours,
Hsin-Lin

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Re: [gmx-users] g_rms on CA atoms only, with and without mass weighting -nomw

[Jan Domanski]

On 07/04/2012 08:34 PM, Mark Abraham wrote:
> On 5/07/2012 10:11 AM, Jan Domanski wrote:
>> (BTW, the g_rms -h mentions something about a '-debug flag' but it
>> seems not to be working.)
> 
> See manual D.1 - the -debug flag takes an argument.
> 
Ah, I see... yes, sorry.

> 
> This is expected. See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic. Mass
> weighting changes the manner in which round-off error accumulates.
> Double precision is less affected by this. Your g_rms is single
> precision, and apparently MDAnalysis is double.
> 

Alright, thanks!

Jan

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Re: [gmx-users] g_rms on CA atoms only, with and without mass weighting -nomw

[Mark Abraham]

On 5/07/2012 10:11 AM, Jan Domanski wrote:

Hi,

I'm using gromacs 4.5.4 and I've got a detailed question on how the mass
weighting works.

Given a trajectory and a pdb from
http://code.google.com/p/mdanalysis/source/browse/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb
http://code.google.com/p/mdanalysis/source/browse/testsuite/MDAnalysisTests/data/adk_oplsaa.trr

I called the following
structure="adk_oplsaa.pdb"
trajectory="adk_oplsaa.trr"
g_rms -s $structure -f $trajectory -o d_rmsd.xvg << EOF
3
3
EOF

g_rms -nomw -s $structure -f $trajectory -o d_rmsd_nomw.xvg << EOF
3
3
EOF

I was expecting the RMSD values to be identical: all the CA
atoms have identical weights with the -mw flag on, which (to my mind)
should be yield same results to when -nomw is specified and the same set
of atoms is selected. The question: is this an unreasonable expectation?

sdiff d_rmsd.xvg  d_rmsd_nomw.xvg  | tail # consistent only for 5 sig figs

   0.0000.369 |   0.0000.368
100.0760.9818456 | 100.0760.9818469
200.1530.8223789 | 200.1530.8223798
300.0000.6450028 | 300.0000.6450034
400.3050.8285408 | 400.3050.8285414
500.3051.9386379 | 500.3051.9386411
600.0001.6888058 | 600.0001.6888076
700.6101.6885630 | 700.6101.6885644
800.6101.8211102 | 800.6101.820
900.6102.1306074 | 900.6102.1306095

(BTW, the g_rms -h mentions something about a '-debug flag' but it
seems not to be working.)


See manual D.1 - the -debug flag takes an argument.



As a check, I've used MDAnalysis 0.7.6-devel
(http://mdanalysis.googlecode.com) and the following code to get RMSD on
the same data, which was consistent over 14 sig figs.

from MDAnalysis import *
from MDAnalysis.analysis.align import *
conf = "adk_oplsaa.pdb"
traj = "adk_oplsaa.trr"
ref = Universe(conf)
mob = Universe(conf, traj)
rms_fit_trj(mob, ref, select="name CA", rmsdfile="rmsd.dat",
mass_weighted=True)
rms_fit_trj(mob, ref, select="name CA", rmsdfile="rmsd_nomw.dat",
mass_weighted=False)

sdiff rmsd.dat  rmsd_nomw.dat # consistent over 14 sig figs
3.686669177327545608e-04 |  3.686671021799712840e-04
9.818467126090068220e+00 |  9.818467126090039798e+00
8.223796870415890581e+008.223796870415890581e+00
6.450033517100112412e+00 |  6.450033517100091096e+00
8.285414822442923821e+00 |  8.285414822442906058e+00
1.938640271585943964e+01 |  1.938640271585941832e+01
1.688807649241958941e+01 |  1.688807649241956454e+01
1.688564785098214571e+01 |  1.688564785098212795e+01
1.82456215330549e+01 |  1.82456215327706e+01
2.130609827021595137e+01 |  2.130609827021593006e+01

Thanks for helping me figure it out guys,


This is expected. See 
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic. Mass 
weighting changes the manner in which round-off error accumulates. 
Double precision is less affected by this. Your g_rms is single 
precision, and apparently MDAnalysis is double.


Mark

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[gmx-users] g_rms on CA atoms only, with and without mass weighting -nomw

[Jan Domanski]

Hi,

I'm using gromacs 4.5.4 and I've got a detailed question on how the mass
weighting works.

Given a trajectory and a pdb from
http://code.google.com/p/mdanalysis/source/browse/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb
http://code.google.com/p/mdanalysis/source/browse/testsuite/MDAnalysisTests/data/adk_oplsaa.trr

I called the following
structure="adk_oplsaa.pdb"
trajectory="adk_oplsaa.trr"
g_rms -s $structure -f $trajectory -o d_rmsd.xvg << EOF
3
3
EOF

g_rms -nomw -s $structure -f $trajectory -o d_rmsd_nomw.xvg << EOF
3
3
EOF

I was expecting the RMSD values to be identical: all the CA
atoms have identical weights with the -mw flag on, which (to my mind)
should be yield same results to when -nomw is specified and the same set
of atoms is selected. The question: is this an unreasonable expectation?

sdiff d_rmsd.xvg  d_rmsd_nomw.xvg  | tail # consistent only for 5 sig figs

  0.0000.369 |   0.0000.368
100.0760.9818456 | 100.0760.9818469
200.1530.8223789 | 200.1530.8223798
300.0000.6450028 | 300.0000.6450034
400.3050.8285408 | 400.3050.8285414
500.3051.9386379 | 500.3051.9386411
600.0001.6888058 | 600.0001.6888076
700.6101.6885630 | 700.6101.6885644
800.6101.8211102 | 800.6101.820
900.6102.1306074 | 900.6102.1306095

(BTW, the g_rms -h mentions something about a '-debug flag' but it
seems not to be working.)

As a check, I've used MDAnalysis 0.7.6-devel
(http://mdanalysis.googlecode.com) and the following code to get RMSD on
the same data, which was consistent over 14 sig figs.

from MDAnalysis import *
from MDAnalysis.analysis.align import *
conf = "adk_oplsaa.pdb"
traj = "adk_oplsaa.trr"
ref = Universe(conf)
mob = Universe(conf, traj)
rms_fit_trj(mob, ref, select="name CA", rmsdfile="rmsd.dat",
mass_weighted=True)
rms_fit_trj(mob, ref, select="name CA", rmsdfile="rmsd_nomw.dat",
mass_weighted=False)

sdiff rmsd.dat  rmsd_nomw.dat # consistent over 14 sig figs
3.686669177327545608e-04 |  3.686671021799712840e-04
9.818467126090068220e+00 |  9.818467126090039798e+00
8.223796870415890581e+008.223796870415890581e+00
6.450033517100112412e+00 |  6.450033517100091096e+00
8.285414822442923821e+00 |  8.285414822442906058e+00
1.938640271585943964e+01 |  1.938640271585941832e+01
1.688807649241958941e+01 |  1.688807649241956454e+01
1.688564785098214571e+01 |  1.688564785098212795e+01
1.82456215330549e+01 |  1.82456215327706e+01
2.130609827021595137e+01 |  2.130609827021593006e+01

Thanks for helping me figure it out guys,


Jan
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Re: [gmx-users] g_rms -bm

[Kowsar Bagherzadeh]

Dear Justin
 
Thank you very muchh
 
Sogol



From: Justin A. Lemkul 
To: Kowsar Bagherzadeh ; Discussion list for GROMACS 
users  
Sent: Thursday, May 24, 2012 9:59 AM
Subject: Re: [gmx-users] g_rms -bm



On 5/24/12 7:24 AM, Kowsar Bagherzadeh wrote:
> 
> 
> Dear Users,
> I am trying to analyze a ligand-protein simulation results. I read in the 
> manual
> that using g_rms command with –bm option produces a matrix of average bond 
> angle
> deviations. And only bonds between atoms in the comparison groups are
> considered. Does it mean that it is for the bonds and their angles that are
> already in existence? (Not the ones that may be formed throughout simulation, 
> I
> mean the ligand may for example interact with residues through H-bonds) .I 
> have

In this context, a "bond" means an actual chemical bond.  A hydrogen bond is a 
nonbonded interaction.

> made a group in my index file named Active site (including only the active 
> site
> residues), and I have a LIG group as well. If I choose these two groups for
> g_rms with this command:
> /g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx**/
> Does it show me how the ligand affects the active site residues bond angles?

Potentially.

> And one more question, how can I study the ligand orientation in the active 
> site?

That depends on how you define orientation - internal metrics like dihedrals or 
angles between planes of groups in the ligand, relative measurements like its 
position with respect to protein residues, etc.  All analysis tools are listed 
in the manual, Chapter 8 and Appendix D.  It's quite a lot to read, but you'll 
be able to identify all the various things you can analyze and how the 
information might be connected across different analysis routines.

-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_rms -bm

[Justin A. Lemkul]

On 5/24/12 7:24 AM, Kowsar Bagherzadeh wrote:



Dear Users,
I am trying to analyze a ligand-protein simulation results. I read in the manual
that using g_rms command with –bm option produces a matrix of average bond angle
deviations. And only bonds between atoms in the comparison groups are
considered. Does it mean that it is for the bonds and their angles that are
already in existence? (Not the ones that may be formed throughout simulation, I
mean the ligand may for example interact with residues through H-bonds) .I have


In this context, a "bond" means an actual chemical bond.  A hydrogen bond is a 
nonbonded interaction.



made a group in my index file named Active site (including only the active site
residues), and I have a LIG group as well. If I choose these two groups for
g_rms with this command:
/g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx**/
Does it show me how the ligand affects the active site residues bond angles?


Potentially.


And one more question, how can I study the ligand orientation in the active 
site?


That depends on how you define orientation - internal metrics like dihedrals or 
angles between planes of groups in the ligand, relative measurements like its 
position with respect to protein residues, etc.  All analysis tools are listed 
in the manual, Chapter 8 and Appendix D.  It's quite a lot to read, but you'll 
be able to identify all the various things you can analyze and how the 
information might be connected across different analysis routines.


-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_rms -bm

[Kowsar Bagherzadeh]

Dear Users, 
I am trying to analyze a ligand-protein simulation results. I read in the 
manual that using g_rms command with –bm option produces a matrix of average 
bond angle deviations. And only bonds between atoms in the comparison groups 
are considered.  Does it mean that it is for the bonds and their angles that 
are already in existence? (Not the ones that may be formed throughout 
simulation, I mean the ligand may for example interact with residues through 
H-bonds) .I have made a group in my index file named Active site (including 
only the active site residues), and I have a LIG group as well. If I choose 
these two groups for g_rms with this command:
g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx
Does it show me how the ligand affects the active site residues bond angles?
And one more question, how can I study the ligand orientation in the active 
site?
Sogol-- 
gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] g_rms -bm

[Kowsar Bagherzadeh]

Dear Users, 
I am trying to analyze a ligand-protein simulation results. I read in the 
manual that using g_rms command with –bm option produces a matrix of average 
bond angle deviations. And only bonds between atoms in the comparison groups 
are considered.  Does it mean that it is for the bonds and their angles that 
are already in existence? (Not the ones that may be formed throughout 
simulation, I mean the ligand may for example interact with residues through 
H-bonds) .I have made a group in my index file named Active site (including 
only the active site residues), and I have a LIG group as well. If I choose 
these two groups for g_rms with this command:
g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx
Does it show me how the ligand affects the active site residues bond angles?
And one more question, how can I study the ligand orientation in the active 
site?
Sogol-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] g_rms on large amount of data

[khuchtumur bumerdene]

Hi,
I'm using Gromacs 4.5.5 to simulate a protein in explicit solvent.
The simulation is running fine and I have collected 9 100ns simulations.
I'm eliminating the first 50 ns for equilibration and sheer data size.
What I want to do now is to cluster the simulations based on rmsd of
certain residues. I have used make_ndx to select the residues and made a
group.
I have used trjcat -cat option to concatenate the 9 runs into a single
giant .xtc file. In the .xtc file, I only output the protein.
My plan was to use g_rms to create a rmsd.xpm table and using that with
g_cluster. However, when I do run g_rms, it seems like it will take weeks
to finish.
The RMSD matrix size becomes 225000x225000 and my question is: How do you
cluster this much data? Any recommendation would be useful.

Thank you for your time.
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Re: [gmx-users] g_rms matrix between wt and mutant

[Shay Teaching]

Thanks Mark and Justin for your input. it works. For progeny, here's how:

1. In case of multiple, separate chains of protein, generate a *new* tpr X
that does not include chain information.
2. From X generate a new tpr file Y, consisting now only of the group under
scrutiny (for example, backbone. Use tpbconv).
3. Make new index file for Y.
4. Now use trjconv to make xtc1  and xtc2 that consist only on that group.
5. Use g_rms with Y tpr, the generate xtcs, and the new index group.

This should work and avoid the notorious segmentation fault (as long as you
make sure the group you choose, backbone for example, has identical number
of atoms in both xtc1 and xtc2).

-SA
On Tue, Sep 13, 2011 at 11:17 AM, Mark Abraham wrote:

>  On 13/09/2011 6:11 PM, Shay Teaching wrote:
>
> Ok I tried that and it doesn't work:
> There's a fundamental difference between chains/no-chains topology, namely
> the existence of peptide bond between chains, and the different protonation
> state on the termini.
> In the chain-based topology there are several termini, and less peptide
> bonds.
>
> This causes the no-chains-tpr to have different number of atoms, and
> different protonation states.
> I tried using tpbconv to make a backbone-tpr, but it still gets me to
> segmentation fault.
>
>
> The idea behind Justin's original solution is still right. You need to
> provide two sets of corresponding atoms and those sets have to have the same
> size. So you need to construct two index groups that suit what you actually
> want to compare - say, the backbone atoms that are common to the two forms.
> That will require some thought, and playing around with make_ndx (or a text
> editor). Then use those to create subset .tpr and trajectory files as Justin
> suggested. Each form is likely to need its own customized index group to
> make the subset that is correct for it.
>
> Mark
>
>
>
> So thanks, but I don't think it would work.
> -SA
>
> On Mon, Sep 12, 2011 at 11:47 PM, Shay Teaching 
> wrote:
>
>> Thanks, I'll try that, and post again if it works.
>>
>>
>> On Mon, Sep 12, 2011 at 6:20 PM, Justin A. Lemkul wrote:
>>
>>>
>>>
>>> Shay Teaching wrote:
>>>
 When I try to work the command on a small portion of the backbone it
 seems to work just fine. But when I try the entire backbone (which is
 composed of several _separate_ chains) I am getting segmentation fault.
 Any workaround for that, so I can use the entire backbone?

>>>
>>>  Are there chain identifiers separating the proteins?  I don't know if
>>> that would cause the problem, but it's possible.  In that case, I'd suggest
>>> you start with a coordinate file and topology without chain identifiers and
>>> generate a new .tpr file (and then take the backbone atoms only with
>>> tpbconv).
>>>
>>> -Justin
>>>
>>>  Thanks again,
 -Shay


 On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul >>> jalem...@vt.edu>> wrote:



Shay Teaching wrote:

Hi all,
(Gromacs 4.0.7): I am trying to make rms matrix between one Wt
trajectory and one mutant trajectory using the following command:

g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n
wt_backbone.ndx

The file wt_backbone.ndx contains the backbone of the protein
(Backbone indices are identical between wt and mutant).

The result is that I am getting a well deserved error saying
that wt.xtc and mutant.xtc has different number of atoms (the
tpr itself):
Fatal error:
Second trajectory (76128 atoms) does not match the first one
(76129 atoms)

So the question becomes: Is there a (convenient) way to produce
rms-matrix between wt and mutant?
Or perhaps circumvent this problem in some other way?


Use trjconv to write out new trajectories containing only backbone
atoms of each protein, then use tpbconv to write a .tpr file with
only backbone atoms in it (using index groups, if necessary).  Then
run g_rms again with these new trajectories and .tpr file.
 Everything should match if the indices are chosen correctly.

-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<%28540%29%20231-9080>


http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


==__==
-- gmx-users mailing listgmx-users@gromacs.org
 

http://lists.gromacs.org/__mailman/listinfo/gmx

Re: [gmx-users] g_rms matrix between wt and mutant

[Mark Abraham]

On 13/09/2011 6:11 PM, Shay Teaching wrote:

Ok I tried that and it doesn't work:
There's a fundamental difference between chains/no-chains topology, 
namely the existence of peptide bond between chains, and the different 
protonation state on the termini.
In the chain-based topology there are several termini, and less 
peptide bonds.


This causes the no-chains-tpr to have different number of atoms, and 
different protonation states.
I tried using tpbconv to make a backbone-tpr, but it still gets me to 
segmentation fault.


The idea behind Justin's original solution is still right. You need to 
provide two sets of corresponding atoms and those sets have to have the 
same size. So you need to construct two index groups that suit what you 
actually want to compare - say, the backbone atoms that are common to 
the two forms. That will require some thought, and playing around with 
make_ndx (or a text editor). Then use those to create subset .tpr and 
trajectory files as Justin suggested. Each form is likely to need its 
own customized index group to make the subset that is correct for it.


Mark



So thanks, but I don't think it would work.
-SA

On Mon, Sep 12, 2011 at 11:47 PM, Shay Teaching 
mailto:shay.teach...@gmail.com>> wrote:


Thanks, I'll try that, and post again if it works.


On Mon, Sep 12, 2011 at 6:20 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



Shay Teaching wrote:

When I try to work the command on a small portion of the
backbone it seems to work just fine. But when I try the
entire backbone (which is composed of several _separate_
chains) I am getting segmentation fault.
Any workaround for that, so I can use the entire backbone?


Are there chain identifiers separating the proteins?  I don't
know if that would cause the problem, but it's possible.  In
that case, I'd suggest you start with a coordinate file and
topology without chain identifiers and generate a new .tpr
file (and then take the backbone atoms only with tpbconv).

-Justin

Thanks again,
-Shay


On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Shay Teaching wrote:

   Hi all,
   (Gromacs 4.0.7): I am trying to make rms matrix
between one Wt
   trajectory and one mutant trajectory using the
following command:

   g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit
rot+trans -n
   wt_backbone.ndx

   The file wt_backbone.ndx contains the backbone of
the protein
   (Backbone indices are identical between wt and mutant).

   The result is that I am getting a well deserved
error saying
   that wt.xtc and mutant.xtc has different number of
atoms (the
   tpr itself):
   Fatal error:
   Second trajectory (76128 atoms) does not match the
first one
   (76129 atoms)

   So the question becomes: Is there a (convenient)
way to produce
   rms-matrix between wt and mutant?
   Or perhaps circumvent this problem in some other way?


   Use trjconv to write out new trajectories containing
only backbone
   atoms of each protein, then use tpbconv to write a .tpr
file with
   only backbone atoms in it (using index groups, if
necessary).  Then
   run g_rms again with these new trajectories and .tpr file.
Everything should match if the indices are chosen
correctly.

   -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 list gmx-users@gromacs.org

>

http://lists.gromacs.org/__mailman/listinfo/gmx-users

   Please search the archive at
h

Re: [gmx-users] g_rms matrix between wt and mutant

[Shay Teaching]

Ok I tried that and it doesn't work:
There's a fundamental difference between chains/no-chains topology, namely
the existence of peptide bond between chains, and the different protonation
state on the termini.
In the chain-based topology there are several termini, and less peptide
bonds.

This causes the no-chains-tpr to have different number of atoms, and
different protonation states.
I tried using tpbconv to make a backbone-tpr, but it still gets me to
segmentation fault.

So thanks, but I don't think it would work.
-SA

On Mon, Sep 12, 2011 at 11:47 PM, Shay Teaching wrote:

> Thanks, I'll try that, and post again if it works.
>
>
> On Mon, Sep 12, 2011 at 6:20 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> Shay Teaching wrote:
>>
>>> When I try to work the command on a small portion of the backbone it
>>> seems to work just fine. But when I try the entire backbone (which is
>>> composed of several _separate_ chains) I am getting segmentation fault.
>>> Any workaround for that, so I can use the entire backbone?
>>>
>>
>> Are there chain identifiers separating the proteins?  I don't know if that
>> would cause the problem, but it's possible.  In that case, I'd suggest you
>> start with a coordinate file and topology without chain identifiers and
>> generate a new .tpr file (and then take the backbone atoms only with
>> tpbconv).
>>
>> -Justin
>>
>>  Thanks again,
>>> -Shay
>>>
>>>
>>> On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>>
>>>
>>>
>>>Shay Teaching wrote:
>>>
>>>Hi all,
>>>(Gromacs 4.0.7): I am trying to make rms matrix between one Wt
>>>trajectory and one mutant trajectory using the following command:
>>>
>>>g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n
>>>wt_backbone.ndx
>>>
>>>The file wt_backbone.ndx contains the backbone of the protein
>>>(Backbone indices are identical between wt and mutant).
>>>
>>>The result is that I am getting a well deserved error saying
>>>that wt.xtc and mutant.xtc has different number of atoms (the
>>>tpr itself):
>>>Fatal error:
>>>Second trajectory (76128 atoms) does not match the first one
>>>(76129 atoms)
>>>
>>>So the question becomes: Is there a (convenient) way to produce
>>>rms-matrix between wt and mutant?
>>>Or perhaps circumvent this problem in some other way?
>>>
>>>
>>>Use trjconv to write out new trajectories containing only backbone
>>>atoms of each protein, then use tpbconv to write a .tpr file with
>>>only backbone atoms in it (using index groups, if necessary).  Then
>>>run g_rms again with these new trajectories and .tpr file.
>>> Everything should match if the indices are chosen correctly.
>>>
>>>-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
>>>
>>> 
>>> >
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>>>
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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

Re: [gmx-users] g_rms matrix between wt and mutant

[Shay Teaching]

Thanks, I'll try that, and post again if it works.

On Mon, Sep 12, 2011 at 6:20 PM, Justin A. Lemkul  wrote:

>
>
> Shay Teaching wrote:
>
>> When I try to work the command on a small portion of the backbone it seems
>> to work just fine. But when I try the entire backbone (which is composed of
>> several _separate_ chains) I am getting segmentation fault.
>> Any workaround for that, so I can use the entire backbone?
>>
>
> Are there chain identifiers separating the proteins?  I don't know if that
> would cause the problem, but it's possible.  In that case, I'd suggest you
> start with a coordinate file and topology without chain identifiers and
> generate a new .tpr file (and then take the backbone atoms only with
> tpbconv).
>
> -Justin
>
>  Thanks again,
>> -Shay
>>
>>
>> On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Shay Teaching wrote:
>>
>>Hi all,
>>(Gromacs 4.0.7): I am trying to make rms matrix between one Wt
>>trajectory and one mutant trajectory using the following command:
>>
>>g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n
>>wt_backbone.ndx
>>
>>The file wt_backbone.ndx contains the backbone of the protein
>>(Backbone indices are identical between wt and mutant).
>>
>>The result is that I am getting a well deserved error saying
>>that wt.xtc and mutant.xtc has different number of atoms (the
>>tpr itself):
>>Fatal error:
>>Second trajectory (76128 atoms) does not match the first one
>>(76129 atoms)
>>
>>So the question becomes: Is there a (convenient) way to produce
>>rms-matrix between wt and mutant?
>>Or perhaps circumvent this problem in some other way?
>>
>>
>>Use trjconv to write out new trajectories containing only backbone
>>atoms of each protein, then use tpbconv to write a .tpr file with
>>only backbone atoms in it (using index groups, if necessary).  Then
>>run g_rms again with these new trajectories and .tpr file.
>> Everything should match if the indices are chosen correctly.
>>
>>-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/Search
>>
>> >
>> before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
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>>> >.
>>
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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_rms matrix between wt and mutant

[Justin A. Lemkul]

Shay Teaching wrote:
When I try to work the command on a small portion of the backbone it 
seems to work just fine. But when I try the entire backbone (which is 
composed of several _separate_ chains) I am getting segmentation fault.

Any workaround for that, so I can use the entire backbone?


Are there chain identifiers separating the proteins?  I don't know if that would 
cause the problem, but it's possible.  In that case, I'd suggest you start with 
a coordinate file and topology without chain identifiers and generate a new .tpr 
file (and then take the backbone atoms only with tpbconv).


-Justin


Thanks again,
-Shay

On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul > wrote:




Shay Teaching wrote:

Hi all,
(Gromacs 4.0.7): I am trying to make rms matrix between one Wt
trajectory and one mutant trajectory using the following command:

g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n
wt_backbone.ndx

The file wt_backbone.ndx contains the backbone of the protein
(Backbone indices are identical between wt and mutant).

The result is that I am getting a well deserved error saying
that wt.xtc and mutant.xtc has different number of atoms (the
tpr itself):
Fatal error:
Second trajectory (76128 atoms) does not match the first one
(76129 atoms)

So the question becomes: Is there a (convenient) way to produce
rms-matrix between wt and mutant?
Or perhaps circumvent this problem in some other way?


Use trjconv to write out new trajectories containing only backbone
atoms of each protein, then use tpbconv to write a .tpr file with
only backbone atoms in it (using index groups, if necessary).  Then
run g_rms again with these new trajectories and .tpr file.
 Everything should match if the indices are chosen correctly.

-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_rms matrix between wt and mutant

[Shay Teaching]

When I try to work the command on a small portion of the backbone it seems
to work just fine. But when I try the entire backbone (which is composed of
several *separate* chains) I am getting segmentation fault.
Any workaround for that, so I can use the entire backbone?
Thanks again,
-Shay

On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul  wrote:

>
>
> Shay Teaching wrote:
>
>> Hi all,
>> (Gromacs 4.0.7): I am trying to make rms matrix between one Wt trajectory
>> and one mutant trajectory using the following command:
>>
>> g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n
>> wt_backbone.ndx
>>
>> The file wt_backbone.ndx contains the backbone of the protein (Backbone
>> indices are identical between wt and mutant).
>>
>> The result is that I am getting a well deserved error saying that wt.xtc
>> and mutant.xtc has different number of atoms (the tpr itself):
>> Fatal error:
>> Second trajectory (76128 atoms) does not match the first one (76129 atoms)
>>
>> So the question becomes: Is there a (convenient) way to produce rms-matrix
>> between wt and mutant?
>> Or perhaps circumvent this problem in some other way?
>>
>
> Use trjconv to write out new trajectories containing only backbone atoms of
> each protein, then use tpbconv to write a .tpr file with only backbone atoms
> in it (using index groups, if necessary).  Then run g_rms again with these
> new trajectories and .tpr file.  Everything should match if the indices are
> chosen correctly.
>
> -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 
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Re: [gmx-users] g_rms matrix between wt and mutant

[Justin A. Lemkul]

Shay Teaching wrote:

Hi all,
(Gromacs 4.0.7): I am trying to make rms matrix between one Wt 
trajectory and one mutant trajectory using the following command:


g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n 
wt_backbone.ndx


The file wt_backbone.ndx contains the backbone of the protein (Backbone 
indices are identical between wt and mutant).


The result is that I am getting a well deserved error saying that wt.xtc 
and mutant.xtc has different number of atoms (the tpr itself):

Fatal error:
Second trajectory (76128 atoms) does not match the first one (76129 atoms)

So the question becomes: Is there a (convenient) way to produce 
rms-matrix between wt and mutant?

Or perhaps circumvent this problem in some other way?


Use trjconv to write out new trajectories containing only backbone atoms of each 
protein, then use tpbconv to write a .tpr file with only backbone atoms in it 
(using index groups, if necessary).  Then run g_rms again with these new 
trajectories and .tpr file.  Everything should match if the indices are chosen 
correctly.


-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_rms matrix between wt and mutant

[Shay Teaching]

Hi all,
(Gromacs 4.0.7): I am trying to make rms matrix between one Wt trajectory
and one mutant trajectory using the following command:

g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n
wt_backbone.ndx

The file wt_backbone.ndx contains the backbone of the protein (Backbone
indices are identical between wt and mutant).

The result is that I am getting a well deserved error saying that wt.xtc and
mutant.xtc has different number of atoms (the tpr itself):
Fatal error:
Second trajectory (76128 atoms) does not match the first one (76129 atoms)

So the question becomes: Is there a (convenient) way to produce rms-matrix
between wt and mutant?
Or perhaps circumvent this problem in some other way?
I tried looking into g_confrms, but apparently it works only on two frames
instead of trajectories.

Thanks a lot,
-Shay
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Re: [gmx-users] g_rms & g-rmsd

[mohsen ramezanpour]

Dear Dr Tsjerk
Thank you for your notice
I was wrong,I read it again and  understood it now :)
best

On Sat, Mar 19, 2011 at 3:46 PM, Tsjerk Wassenaar  wrote:

> Hi Mohsen. These programs calculate quite different things. Please read
> their manpages. Read them better if you already read them once ;)
>
> Cheers,
>
> Tsjerk
>
> On Mar 19, 2011 12:16 PM, "mohsen ramezanpour" <
> ramezanpour.moh...@gmail.com> wrote:
>
> Dear All
>
>
>
> I have a trajectory(.xtc) and its corresponding .tpr file:
> I used the following commands separately but the results were
> different,Why??
>
> g_rms-f   trajectory.xtc-s   structure.tpr-n index.ndx-o
> rms.xvg
> I choosed   group number 12 (drug in pulling problem) for two choose
>
> g_rmsdist   -f   trajectory.xtc-s   structure.tpr   -o
> rmsdist.xvg
> I choosed the group number 12
>
> Since I didn't determine the reference for g_rms ,I expect the same
> results,because both of them choose the tpr structure as the reference one.
> Am I right?
>
> Thanks in advance
>
>
>
>
>
> --
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Re: [gmx-users] g_rms & g-rmsd

[Tsjerk Wassenaar]

Hi Mohsen. These programs calculate quite different things. Please read
their manpages. Read them better if you already read them once ;)

Cheers,

Tsjerk

On Mar 19, 2011 12:16 PM, "mohsen ramezanpour" 
wrote:

Dear All


I have a trajectory(.xtc) and its corresponding .tpr file:
I used the following commands separately but the results were
different,Why??

g_rms-f   trajectory.xtc-s   structure.tpr-n index.ndx-o
rms.xvg
I choosed   group number 12 (drug in pulling problem) for two choose

g_rmsdist   -f   trajectory.xtc-s   structure.tpr   -o
rmsdist.xvg
I choosed the group number 12

Since I didn't determine the reference for g_rms ,I expect the same
results,because both of them choose the tpr structure as the reference one.
Am I right?

Thanks in advance





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[gmx-users] g_rms & g-rmsd

[mohsen ramezanpour]

Dear All


I have a trajectory(.xtc) and its corresponding .tpr file:
I used the following commands separately but the results were
different,Why??

g_rms-f   trajectory.xtc-s   structure.tpr-n index.ndx-o
rms.xvg
I choosed   group number 12 (drug in pulling problem) for two choose

g_rmsdist   -f   trajectory.xtc-s   structure.tpr   -o
rmsdist.xvg
I choosed the group number 12

Since I didn't determine the reference for g_rms ,I expect the same
results,because both of them choose the tpr structure as the reference one.
Am I right?

Thanks in advance
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Re: [gmx-users] g_rms and g_cluster

[Mark Abraham]

On 09/03/11, shahid nayeem   wrote:
> Hi Justin
> If I make an index group with backbone and CA C N O group of the
> concerned residues and then do least square fitting then do this
> fitting is equivalent to backbone fitting first and then translating
> to coincide CA of the residue of interest. Is there any other
> programme developed for gromacs trajectory analysis where I can do
> backbone fitting first and then translate to coincide CA of residue of
> interest before calculating RMSD.
> 

Group-wise fitting subject to the constraint of particular atoms overlaid 
requires a quite different algorithm from plain group-wise fitting, and is not 
implemented. You can do the plain fit, calculate the relative displacement of 
one CA from another by hand, and do the corresponding translation with 
editconf, but I doubt you're going to learn anything...

Mark


> 
> Shahid Nayeem
> 
> On Thu, Feb 24, 2011 at 7:14 PM, Justin A. Lemkul  wrote:
> >
> >
> > shahid nayeem wrote:
> >>
> >> Dear All
> >>
> >> I want to calculate RMSD of one side chain residue from simulation
> >> trajectory after full backbone alignment as well as translating to
> >> coincide CA of the residue of interest. Is it possible to do with
> >> g_rms both backbone alignment as well as translating to coincide CA.
> >
> > Least-squares fitting is performed on whatever group you choose (i.e.
> > backbone), and the calculation group can then be whatever you want.  You can
> > use trjconv to do translational fitting, but I don't know that you can force
> > g_rms to always align this certain atom and still perform a backbone fit;
> > these two may work against one another, even if the difference is small.
> >
> >> Another clarification is that in gromacs g_cluster how can I use
> >> greedy algorithm for clustering.
> >
> > What is a "greedy" algorithm?  The available methods are described in the
> > manual and/or g_cluster -h.
> >
> > -Justin
> >
> >> Shahid Nayeem
> >
> > --
> > 
> >
> > 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_rms and g_cluster

[shahid nayeem]

Hi Justin
If I make an index group with backbone and CA C N O group of the
concerned residues and then do least square fitting then do this
fitting is equivalent to backbone fitting first and then translating
to coincide CA of the residue of interest. Is there any other
programme developed for gromacs trajectory analysis where I can do
backbone fitting first and then translate to coincide CA of residue of
interest before calculating RMSD.
Shahid Nayeem

On Thu, Feb 24, 2011 at 7:14 PM, Justin A. Lemkul  wrote:
>
>
> shahid nayeem wrote:
>>
>> Dear All
>>
>> I want to calculate RMSD of one side chain residue from simulation
>> trajectory after full backbone alignment as well as translating to
>> coincide CA of the residue of interest. Is it possible to do with
>> g_rms both backbone alignment as well as translating to coincide CA.
>
> Least-squares fitting is performed on whatever group you choose (i.e.
> backbone), and the calculation group can then be whatever you want.  You can
> use trjconv to do translational fitting, but I don't know that you can force
> g_rms to always align this certain atom and still perform a backbone fit;
> these two may work against one another, even if the difference is small.
>
>> Another clarification is that in gromacs g_cluster how can I use
>> greedy algorithm for clustering.
>
> What is a "greedy" algorithm?  The available methods are described in the
> manual and/or g_cluster -h.
>
> -Justin
>
>> Shahid Nayeem
>
> --
> 
>
> 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_RMS: Mismatch of atom number between topology and reference structure

[Mark Abraham]

On 7/03/2011 7:33 PM, Sergio Manzetti wrote:
Hello, I am doing a refolding experiment, but I re-experience the same 
error. First of all, I use pdb2gmx for an input PDB structure, choose 
OPLS/AA force field and vacuum settings (no waters).


Then I amke a box, and start simulations.

What I want to do is to compare the starting unfolded structure of the 
simulation and its changes during the sim (all represented as a 
traj.xtc) to a native folded conformation of the structure. Assuming 
it to be possible, I thought of using g_rms;


g_rms -f native-folded.gro -s topol.tpr


Then I get the same error message:

WARNING: topology has 497 atoms, whereas trajectory has 491

---
Program g_rms, VERSION 4.5.1
Source code file: mshift.c, line: 102

Fatal error:
Molecule in topology has atom numbers below and above natoms (491).

Thing is that both the topology and the trajectory are treated equally 
at the pdb2gmx step. So how can it be?


You've almost certainly mismatched these files. Only your records can 
make sense of what has gone wrong. The source of this folded form has to 
be treated in an equivalent fashion (e.g. with another invocation of 
pdb2gmx) so that the atom ordering and numbering matches.


Mark
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Re: [gmx-users] g_RMS: Mismatch of atom number between topology and reference structure

[Justin A. Lemkul]

Sergio Manzetti wrote:
Hello, I am doing a refolding experiment, but I re-experience the same 
error. First of all, I use pdb2gmx for an input PDB structure, choose 
OPLS/AA force field and vacuum settings (no waters).


Then I amke a box, and start simulations.

What I want to do is to compare the starting unfolded structure of the 
simulation and its changes during the sim (all represented as a 
traj.xtc) to a native folded conformation of the structure. Assuming it 
to be possible, I thought of using g_rms;


g_rms -f native-folded.gro -s topol.tpr


Then I get the same error message:

WARNING: topology has 497 atoms, whereas trajectory has 491

---
Program g_rms, VERSION 4.5.1
Source code file: mshift.c, line: 102

Fatal error:
Molecule in topology has atom numbers below and above natoms (491).



Either (1) you're not saving the right atoms during the simulation (xtc-grps) or 
(2) you're choosing to analyze a non-existent group with g_rms, or a combination 
of both.  For better diagnostics, provide your .mdp file, a description of your 
system, and your g_rms command line.


Thing is that both the topology and the trajectory are treated equally 
at the pdb2gmx step. So how can it be?




pdb2gmx only deals with coordinate files in order to produce the topology.  Your 
trajectory is irrelevant here, but if you've somehow tried to manipulate your 
trajectory or its contents with pdb2gmx, then you can be sure that this is 
what's causing your error.


-Justin


Sergio



--


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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_RMS: Mismatch of atom number between topology and reference structure

[Sergio Manzetti]

Hello, I am doing a refolding experiment, but I re-experience the same
error. First of all, I use pdb2gmx for an input PDB structure, choose
OPLS/AA force field and vacuum settings (no waters).

Then I amke a box, and start simulations.

What I want to do is to compare the starting unfolded structure of the
simulation and its changes during the sim (all represented as a traj.xtc) to
a native folded conformation of the structure. Assuming it to be possible, I
thought of using g_rms;

g_rms -f native-folded.gro -s topol.tpr


Then I get the same error message:

WARNING: topology has 497 atoms, whereas trajectory has 491

---
Program g_rms, VERSION 4.5.1
Source code file: mshift.c, line: 102

Fatal error:
Molecule in topology has atom numbers below and above natoms (491).

Thing is that both the topology and the trajectory are treated equally at
the pdb2gmx step. So how can it be?

Sergio
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Re: [gmx-users] g_rms and g_cluster

[Justin A. Lemkul]

shahid nayeem wrote:

Dear All

I want to calculate RMSD of one side chain residue from simulation
trajectory after full backbone alignment as well as translating to
coincide CA of the residue of interest. Is it possible to do with
g_rms both backbone alignment as well as translating to coincide CA.


Least-squares fitting is performed on whatever group you choose (i.e. backbone), 
and the calculation group can then be whatever you want.  You can use trjconv to 
do translational fitting, but I don't know that you can force g_rms to always 
align this certain atom and still perform a backbone fit; these two may work 
against one another, even if the difference is small.



Another clarification is that in gromacs g_cluster how can I use
greedy algorithm for clustering.


What is a "greedy" algorithm?  The available methods are described in the manual 
and/or g_cluster -h.


-Justin


Shahid Nayeem


--


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_rms and g_cluster

[shahid nayeem]

Dear All

I want to calculate RMSD of one side chain residue from simulation
trajectory after full backbone alignment as well as translating to
coincide CA of the residue of interest. Is it possible to do with
g_rms both backbone alignment as well as translating to coincide CA.
Another clarification is that in gromacs g_cluster how can I use
greedy algorithm for clustering.
Shahid Nayeem
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Re: [gmx-users] g_rms question

[Tsjerk Wassenaar]

Hi Udi,

Square the numbers... It's Root Mean Square Deviation, right? But roots
don't add up like that.

Cheers,

Tsjerk

On Aug 12, 2010 12:02 AM, "udi"  wrote:

 Hi gromacs users,

I’m simulating a protein that consists of 5 domains. I have calculated the
whole protein’s backbone RMSD by entering ‘4’ twice.

Now, I would like to calculate the contribution of every domain i.e. if the
whole protein’s RMSD in the first frame is  1nm, then how is this 1nm
distributed between the 5 domains.

I have created 5 groups in the index file of the backbone of every domain
and calculated the RMSD by first entering ‘4’ in order to fit the whole
backbone and entered the domains backbone groups in the second entry. (5
different calculations). The problem is that the values I get from the
domains do not add up to the whole backbone RMSD values!!! What am doing
wrong?



Thanks from advanced

Chears



Udi

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[gmx-users] g_rms question

[udi]

Hi gromacs users,

I'm simulating a protein that consists of 5 domains. I have calculated the
whole protein's backbone RMSD by entering '4' twice.

Now, I would like to calculate the contribution of every domain i.e. if the
whole protein's RMSD in the first frame is  1nm, then how is this 1nm
distributed between the 5 domains.

I have created 5 groups in the index file of the backbone of every domain
and calculated the RMSD by first entering '4' in order to fit the whole
backbone and entered the domains backbone groups in the second entry. (5
different calculations). The problem is that the values I get from the
domains do not add up to the whole backbone RMSD values!!! What am doing
wrong? 

 

Thanks from advanced

Chears

 

Udi 

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Re: [gmx-users] g_rms warning

[Tsjerk Wassenaar]

Hi Carla,

You'll have to use index groups to extract a trajectory and reference
that correspond. If you have those you can get on with the RMSD.

Cheers,

Tsjerk

On Mon, Mar 8, 2010 at 11:44 AM, Carla Jamous  wrote:
> Hi everyone, please I just need a precision:
>
> I need to calculate the RMSD of a trajectory by comparing it to a reference
> structure that doesn't have the same number of atoms.
> Gromacs is calculating the RMSD, but meanwhile it generates this
> warning:"topology has 4839 atoms, whereas trajectory has 4834"
>
> Does it really affect the result of my RMSD or can I ignore it?
>
> Thanks
> Carla
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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[gmx-users] g_rms warning

[Carla Jamous]

Hi everyone, please I just need a precision:

I need to calculate the RMSD of a trajectory by comparing it to a reference
structure that doesn't have the same number of atoms.
Gromacs is calculating the RMSD, but meanwhile it generates this
warning:"topology has 4839 atoms, whereas trajectory has 4834"

Does it really affect the result of my RMSD or can I ignore it?

Thanks
Carla
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Re: [gmx-users] g_rms (rmsd vs residue no)

[João M . Damas]

Hi Leila,

Try the -od option in g_rmsf.

Regards,
João

On Wed, Dec 9, 2009 at 8:56 AM, leila karami wrote:

> Hi
>
> g_rms gives us a xvg file containing rmsd vs time.
>
> I want obtain rmsd vs residue number.
>
> what option should be used with g_rms?
>
> Any help will highly appreciated!
>
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PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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Re: [gmx-users] g_rms (rmsd vs residue no)

[Tsjerk Wassenaar]

Hi Leila,

There is no such option. This has been discussed on the list quite
recently. You can try to be creative with index groups to get what you
want.

Cheers,

Tsjerk


On Wed, Dec 9, 2009 at 9:56 AM, leila karami  wrote:
> Hi
>
> g_rms gives us a xvg file containing rmsd vs time.
>
> I want obtain rmsd vs residue number.
>
> what option should be used with g_rms?
>
> Any help will highly appreciated!
>
> --
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-- 
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Computational Chemist
Medicinal Chemist
Neuropharmacologist
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[gmx-users] g_rms (rmsd vs residue no)

[leila karami]

Hi

g_rms gives us a xvg file containing rmsd vs time.

I want obtain rmsd vs residue number.

what option should be used with g_rms?

Any help will highly appreciated!
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Re: [gmx-users] g_rms (was H-Db error)

[Justin A. Lemkul]

If you are changing the topic, please start a new thread to avoid confusion in 
the archive.


When running g_rms, you choose the group for analysis; there is no default.

-Justin

nikhil damle wrote:

Hi,
I want to know, by default g_rms calculates RMSD on which atoms set - 
backbone, all atoms or c-alphas ? How do i modify these settings ?


Regards,
Nikhil


*From:* Mark Abraham 
*To:* Discussion list for GROMACS users 
*Sent:* Monday, 20 July, 2009 7:35:29 AM
*Subject:* Re: [gmx-users] H-Db error

nikhil damle wrote:
 > This is how i have modified the entry as i myself created the 
parameter file for phosphothreonine. This is normal NH hydrogen n no 
extra added=>directly copied from threonine. So y there is an error msg 
? i added this residue in aminoacids.dat file as well. and 2ns line is 
tab separated. Is there any other formatting to b done ??

 >
 >
 > TPO1
 > 1  1  H  N  -C  CA
 >
 >
 >
 > This is error msg i get: (I also checked h_db.c programme but could 
not get much help abt the error msg)

 > ---
 > All occupancies are one
 > Opening library file 
/home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.atp

 > Atomtype 1
 > Reading residue database... (ffG43a1)
 > Opening library file 
/home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.rtp

 > Residue 97
 > Sorting it all out...
 > Opening library file 
/home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.hdb

 >
 > ---
 > Program pdb2gmx, VERSION 4.0.5
 > Source code file: h_db.c, line: 162
 >
 > Fatal error:
 > Error reading from file ffG43a1
 > 
---


That looks weird. Try spaces, not tabs. What does "pdb2gmx -debug 
-yourflags" say? If you have an empty line at the end, try removing it.


Mark
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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_rms: Too many iterations in routine JACOBI

[nishtha pandey]

Hello,
 Thank you for your reply. I used .tpr file genarated from grompp for
mdrun which generated the .trr file.
I have not specified xtc-grps.
Regards,
Nishtha

On Sat, Jan 24, 2009 at 11:02 PM, Tsjerk Wassenaar wrote:

> Hi,
>
> On Sat, Jan 24, 2009 at 12:04 PM, nishtha pandey 
> wrote:
> > Hello everyone,
> >  While trying to do the RMSD analysis of my
> trajectory
> > file I am facing the error " Too many iterations in routine JACOBI". I
> have
> > gone through the archives which suggests that such problem arises if
> there
> > is mismatch between the reference structure and trajectory. However in my
> > case the problem lies somewhere else because, using the same .tpr file
> and
> > .trr file I have done RMSD analysis earlier also and it worked fine.
>
> The .tpr and the .trr files will correspond per definition, provided
> the former is used to generate the latter. This is not the case for
> the .xtc. My guess is you do have a mismatch. Did you specify
> xtc-grps? In that case you might want to extract a corresponding
> reference structure from your .tpr.
>
> Hope it helps,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
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Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

[Tsjerk Wassenaar]

Hi,

On Sat, Jan 24, 2009 at 12:04 PM, nishtha pandey  wrote:
> Hello everyone,
>  While trying to do the RMSD analysis of my trajectory
> file I am facing the error " Too many iterations in routine JACOBI". I have
> gone through the archives which suggests that such problem arises if there
> is mismatch between the reference structure and trajectory. However in my
> case the problem lies somewhere else because, using the same .tpr file and
> .trr file I have done RMSD analysis earlier also and it worked fine.

The .tpr and the .trr files will correspond per definition, provided
the former is used to generate the latter. This is not the case for
the .xtc. My guess is you do have a mismatch. Did you specify
xtc-grps? In that case you might want to extract a corresponding
reference structure from your .tpr.

Hope it helps,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

[David van der Spoel]

nishtha pandey wrote:

Hello,
The molecule is not planar it is 3D. Also I would like to 
mention that the same reference structure gave me result earlier.  I 
chose protein as group for least square fit and CA for RMSD calculation.

Thanks and regards,
try extracting the trajectory frame at the time point where it is going 
wrong and use g_confrms (it uses the same algorithm).
The reference structure is not the problem, it is the other one (most 
likely). Maybe your simulation crashed.



Nishtha

On Sat, Jan 24, 2009 at 4:51 PM, David van der Spoel 
mailto:sp...@xray.bmc.uu.se>> wrote:


nishtha pandey wrote:

Hi,
   Thank you for your response. It is a protein molecule
containing 610 amino acid residues.


you didn't answer my question.
please inspect the molecular structure at the time point where the
error  occurs.

Thanks and regards,
Nishtha


On Sat, Jan 24, 2009 at 4:37 PM, David van der Spoel
mailto:sp...@xray.bmc.uu.se>
>> wrote:

   nishtha pandey wrote:

   Hello everyone,
   While trying to do the RMSD analysis
of my
   trajectory file I am facing the error " Too many
iterations in
   routine JACOBI". I have gone through the archives which
suggests
   that such problem arises if there is mismatch between the
   reference structure and trajectory. However in my case the
   problem lies somewhere else because, using the same .tpr file
   and .trr file I have done RMSD analysis earlier also and it
   worked fine.  The g_rms program is giving error but, for the
   same set of input files g_rmsdist is working fine.

   g_rmsdist doesn't use lsq fitting.

   Is you molecule linear or planar? (i.e. not 3D)?

  Kindly help.
   Regards,
   Nishtha


 
 


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   Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
   Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax:
+4618511755.
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Molec. Biophys. group, Dept. of Cell &

Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

[nishtha pandey]

Hello,
The molecule is not planar it is 3D. Also I would like to mention
that the same reference structure gave me result earlier.  I chose protein
as group for least square fit and CA for RMSD calculation.
Thanks and regards,
Nishtha

On Sat, Jan 24, 2009 at 4:51 PM, David van der Spoel
wrote:

> nishtha pandey wrote:
>
>> Hi,
>>Thank you for your response. It is a protein molecule containing 610
>> amino acid residues.
>>
>
> you didn't answer my question.
> please inspect the molecular structure at the time point where the error
>  occurs.
>
>  Thanks and regards,
>> Nishtha
>>
>> On Sat, Jan 24, 2009 at 4:37 PM, David van der Spoel <
>> sp...@xray.bmc.uu.se > wrote:
>>
>>nishtha pandey wrote:
>>
>>Hello everyone,
>>While trying to do the RMSD analysis of my
>>trajectory file I am facing the error " Too many iterations in
>>routine JACOBI". I have gone through the archives which suggests
>>that such problem arises if there is mismatch between the
>>reference structure and trajectory. However in my case the
>>problem lies somewhere else because, using the same .tpr file
>>and .trr file I have done RMSD analysis earlier also and it
>>worked fine.  The g_rms program is giving error but, for the
>>same set of input files g_rmsdist is working fine.
>>
>>g_rmsdist doesn't use lsq fitting.
>>
>>Is you molecule linear or planar? (i.e. not 3D)?
>>
>>   Kindly help.
>>Regards,
>>Nishtha
>>
>>
>>
>>  
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
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>>http://www.gromacs.org/mailman/listinfo/gmx-users
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>>
>>
>>--David van der Spoel, Ph.D., Professor of Biology
>>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
>> University.
>>Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
>>sp...@xray.bmc.uu.se 
>> sp...@gromacs.org    http://folding.bmc.uu.se
>>___
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>>
>> 
>>
>> ___
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>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

[David van der Spoel]

nishtha pandey wrote:

Hi,
Thank you for your response. It is a protein molecule containing 610 
amino acid residues.


you didn't answer my question.
please inspect the molecular structure at the time point where the error 
 occurs.



Thanks and regards,
Nishtha

On Sat, Jan 24, 2009 at 4:37 PM, David van der Spoel 
mailto:sp...@xray.bmc.uu.se>> wrote:


nishtha pandey wrote:

Hello everyone,
While trying to do the RMSD analysis of my
trajectory file I am facing the error " Too many iterations in
routine JACOBI". I have gone through the archives which suggests
that such problem arises if there is mismatch between the
reference structure and trajectory. However in my case the
problem lies somewhere else because, using the same .tpr file
and .trr file I have done RMSD analysis earlier also and it
worked fine.  The g_rms program is giving error but, for the
same set of input files g_rmsdist is working fine.

g_rmsdist doesn't use lsq fitting.

Is you molecule linear or planar? (i.e. not 3D)?

   Kindly help.
Regards,
Nishtha




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-- 
David van der Spoel, Ph.D., Professor of Biology

Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se   
 sp...@gromacs.org    http://folding.bmc.uu.se

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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

[nishtha pandey]

Hi,
Thank you for your response. It is a protein molecule containing 610
amino acid residues.
Thanks and regards,
Nishtha

On Sat, Jan 24, 2009 at 4:37 PM, David van der Spoel
wrote:

> nishtha pandey wrote:
>
>> Hello everyone,
>> While trying to do the RMSD analysis of my trajectory
>> file I am facing the error " Too many iterations in routine JACOBI". I have
>> gone through the archives which suggests that such problem arises if there
>> is mismatch between the reference structure and trajectory. However in my
>> case the problem lies somewhere else because, using the same .tpr file and
>> .trr file I have done RMSD analysis earlier also and it worked fine.  The
>> g_rms program is giving error but, for the same set of input files g_rmsdist
>> is working fine.
>>
> g_rmsdist doesn't use lsq fitting.
>
> Is you molecule linear or planar? (i.e. not 3D)?
>
>>Kindly help.
>> Regards,
>> Nishtha
>>
>>
>> 
>>
>> ___
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>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

[David van der Spoel]

nishtha pandey wrote:

Hello everyone,
 While trying to do the RMSD analysis of my 
trajectory file I am facing the error " Too many iterations in routine 
JACOBI". I have gone through the archives which suggests that such 
problem arises if there is mismatch between the reference structure and 
trajectory. However in my case the problem lies somewhere else because, 
using the same .tpr file and .trr file I have done RMSD analysis earlier 
also and it worked fine.  The g_rms program is giving error but, for the 
same set of input files g_rmsdist is working fine.

g_rmsdist doesn't use lsq fitting.

Is you molecule linear or planar? (i.e. not 3D)?

Kindly help.
Regards,
Nishtha




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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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[gmx-users] g_rms: Too many iterations in routine JACOBI

[nishtha pandey]

Hello everyone,
 While trying to do the RMSD analysis of my trajectory
file I am facing the error " Too many iterations in routine JACOBI". I have
gone through the archives which suggests that such problem arises if there
is mismatch between the reference structure and trajectory. However in my
case the problem lies somewhere else because, using the same .tpr file and
.trr file I have done RMSD analysis earlier also and it worked fine.  The
g_rms program is giving error but, for the same set of input files g_rmsdist
is working fine.
Kindly help.
Regards,
Nishtha
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Re: [gmx-users] g_rms

[Tsjerk Wassenaar]

Hi Tatsiana,

No.

g_rms requires the input trajectory and the reference structure to
match. Actually, the trajectory (if .xtc format) does not even contain
information regarding the atoms; only coordinates. Tools depend wholly
on the reference structure for information on atom/residue names, etc.

Cheers,

Tsjerk

On Mon, Nov 10, 2008 at 5:36 PM, Tatsiana Kirys <[EMAIL PROTECTED]> wrote:
> Hi,
>
> i use g_rms to calculate rms,
>
> as reference structure (-s) i use myprotein.pdb file
> and trajectory (-f) is a trajectiry  after MD MDprotein.pdb.
>
> The thing is that myprotein.pdb  and  MDprotein.pdb have the same atoms BUT 
> their order within a residue is DIFFERENT.
> example:
> myprotein.pdb:
> ATOM  1  N   ALA E   1  18.858 -22.883  26.306  1.00  0.00
> ATOM  2  CA  ALA E   1  19.106 -24.277  26.027  1.00  0.00
> ATOM  3  C   ALA E   1  20.206 -24.458  25.006  1.00  0.00
> ATOM  4  O   ALA E   1  20.156 -23.801  23.972  1.00  0.00
> ATOM  5  CB  ALA E   1  17.865 -24.819  25.301  1.00  0.00
>
> MDprotein.pdb:
> ATOM  1  N   ALA 1  18.861  24.179  26.290  1.00  0.00
> ATOM  2  CA  ALA 1  18.978  22.741  26.011  1.00  0.00
> ATOM  3  CB  ALA 1  17.670  22.190  25.440  1.00  0.00
> ATOM  4  C   ALA 1  20.069  22.592  24.949  1.00  0.00
> ATOM  5  O   ALA 1  20.120  23.450  24.070  1.00  0.00
>
> whether g_rms work correct in this case?
>
> g_rms -s myprotein.pdb -f MDprotein.pdb
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] g_rms

[Tatsiana Kirys]

Hi,

i use g_rms to calculate rms, 

as reference structure (-s) i use myprotein.pdb file
and trajectory (-f) is a trajectiry  after MD MDprotein.pdb.

The thing is that myprotein.pdb  and  MDprotein.pdb have the same atoms BUT 
their order within a residue is DIFFERENT.
example:
myprotein.pdb:
ATOM  1  N   ALA E   1  18.858 -22.883  26.306  1.00  0.00  
 
ATOM  2  CA  ALA E   1  19.106 -24.277  26.027  1.00  0.00  
 
ATOM  3  C   ALA E   1  20.206 -24.458  25.006  1.00  0.00  
 
ATOM  4  O   ALA E   1  20.156 -23.801  23.972  1.00  0.00  
 
ATOM  5  CB  ALA E   1  17.865 -24.819  25.301  1.00  0.00

MDprotein.pdb:
ATOM  1  N   ALA 1  18.861  24.179  26.290  1.00  0.00
ATOM  2  CA  ALA 1  18.978  22.741  26.011  1.00  0.00
ATOM  3  CB  ALA 1  17.670  22.190  25.440  1.00  0.00
ATOM  4  C   ALA 1  20.069  22.592  24.949  1.00  0.00
ATOM  5  O   ALA 1  20.120  23.450  24.070  1.00  0.00

whether g_rms work correct in this case?

g_rms -s myprotein.pdb -f MDprotein.pdb 
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Re: [gmx-users] g_rms

[Tsjerk Wassenaar]

Hi Tania,

The boolean options to the gromacs programs are (usually) set using
(e.g.) -mw | -nomw

Cheers,

Tsjerk


On Sat, Nov 8, 2008 at 5:00 AM, Mark Abraham <[EMAIL PROTECTED]> wrote:
> Tatsiana Kirys wrote:
>>
>> Hi,
>>
>> i got strange results using g_rms.
>> Does it by default uses mass weighting for superposition? I wrote my own
>> script to calculate rmsd without mass weighting and it gives different
>> results then using g_rms. If it uses mass weighting for superposition how
>> not not use it? i tried select "-mw no", but it doesn't work.
>
> As always, g_rms -h explains some relevant issues here.
>
> Also, "it doesn't work" is also a useless description for helping us help
> you. :-)
>
> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] g_rms

[Mark Abraham]

Tatsiana Kirys wrote:

Hi,

i got strange results using g_rms.
Does it by default uses mass weighting for superposition? 
I wrote my own script to calculate rmsd without mass weighting and it gives different results then using g_rms. 
If it uses mass weighting for superposition how not not use it? i tried select "-mw no", but it doesn't work.


As always, g_rms -h explains some relevant issues here.

Also, "it doesn't work" is also a useless description for helping us 
help you. :-)


Mark
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[gmx-users] g_rms

[Tatsiana Kirys]

Hi,

i got strange results using g_rms.
Does it by default uses mass weighting for superposition? 
I wrote my own script to calculate rmsd without mass weighting and it gives 
different results then using g_rms. 
If it uses mass weighting for superposition how not not use it? i tried select 
"-mw no", but it doesn't work.


namy thanks
Tania
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Re: [gmx-users] G_RMS after Replica exchange

[Tsjerk Wassenaar]

Hi Ricardo,

Please give your exact command lines and the error you're refering to.
The way it is now, you provide too little information for us to assess
the origin of your problem.

Cheers,

Tsjerk

On Tue, Sep 2, 2008 at 8:53 PM, Ricardo Soares <[EMAIL PROTECTED]> wrote:
> Hello everyone,
>
> I perform a simulation at 300K, then after 50 ns, I took the final structure
> and performed another one, but now at 274K. How can I compare this second
> trajectory's RMSD with the initial structure from the first simulation
> (300K)?
> If I compare with the first tpr file or the initial pdb file, I get an
> error. If I compare with the second simulation's tpr file, it is done, but
> the comparison is not with the T=0.
> Any ideas?
>
> Thanks!
>
> --
> ___
>
> Ricardo Oliveira dos Santos Soares
> Post-graduation Student in Biological Physics
> University of Sao Paulo - USP
> Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
> Phone: 55 (16) 3602-4840
> Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
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>
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-- 
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Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] G_RMS after Replica exchange

[Ricardo Soares]

Hello everyone,

I perform a simulation at 300K, then after 50 ns, I took the final 
structure and performed another one, but now at 274K. How can I compare 
this second trajectory's RMSD with the initial structure from the first 
simulation (300K)?
If I compare with the first tpr file or the initial pdb file, I get an 
error. If I compare with the second simulation's tpr file, it is done, 
but the comparison is not with the T=0.

Any ideas?

Thanks!

--
___

Ricardo Oliveira dos Santos Soares
Post-graduation Student in Biological Physics
University of Sao Paulo - USP
Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
Phone: 55 (16) 3602-4840
Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
___

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[gmx-users] G_RMS for different simulations

[Ricardo Soares]

Hi everyone,

I need to compare a traj.xtc file from a simulation (say, A), with a 
starting structure from *another* simulation (say, B). The protein is 
the same, but the temperatures aren't.


I tried the fallowing, with no success:

g_rms -s simulation*A*.tpr -f simulation*B*.xtc

Any ideas?

Thanks!

--
___

Ricardo Oliveira dos Santos Soares
Post-graduation Student in Biological Physics
University of Sao Paulo - USP
Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
Phone: 55 (16) 3602-4840
Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
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[gmx-users] G_RMS for different simulations

[Ricardo Soares]

Ok, solved it simply by using the confout.gro for another simulation 
instead of its tpr file.

Thanks anyway!

--
___

Ricardo Oliveira dos Santos Soares
Post-graduation Student in Biological Physics
University of Sao Paulo - USP
Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
Phone: 55 (16) 3602-4840
Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
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Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

[Tsjerk Wassenaar]

Hi JS RED,

This usually indicates that you have a mismatch between your reference
structure and your trajectory, which is logical as you extracted a
specific set of coordinates from the trajectory, but used an original
(complete) gro file.

Hope it helps,

Tsjerk

On Thu, May 8, 2008 at 9:18 AM, minnale <[EMAIL PROTECTED]> wrote:
>
>
>
>  Hi all,
>  1)I made make_ndx file for my protein because i want to plot rmsd for
> specific residues in protein, so I have givenlike this 1 & r 50-80
>
>  2)Then I have used trjcat -f 1ns.xtc 2ns.xtc 3ns.xtc -n r_50_80.ndx
> -settime -o trjout , here I selected
>  Protein_&_r_50-80
>  this command ran without error,
>
>  3)After,
>  g_rms -f trjout.xtc -pbc -s em_inti.gro -pbc -o rms_3ns
>  Select group for least squares fit - 3 c-alpha
>  Select group for RMSD calculation - 3  c-alpha
>  it showed following error
>
>  Program g_rms, VERSION 3.3.1
>  Source code file: nrjac.c, line: 129
>
>  Fatal error:
>  Error: Too many iterations in routine JACOBI
>  I have searched in gmx archives regarding this problem , I found that
> mismatch between trjactory and reference structure file, but in my case both
> are matched atoms
>
>  Is there any mistake in either selecting options of making index file or I
> have given wrong option while using g_rms
>
>  Pls suggest me
>  Thanks in advance.
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] g_rms: Too many iterations in routine JACOBI

[minnale]

  
Hi all, 
1)I made make_ndx file for my protein because i want to plot rmsd for specific 
residues in protein, so I have givenlike this 1 & r 50-80

2)Then I have used trjcat -f 1ns.xtc 2ns.xtc 3ns.xtc -n r_50_80.ndx -settime -o 
trjout , here I selected 
Protein_&_r_50-80
this command ran without error,

3)After, 
g_rms -f trjout.xtc -pbc -s em_inti.gro -pbc -o rms_3ns
Select group for least squares fit - 3 c-alpha
Select group for RMSD calculation - 3  c-alpha
it showed following error

Program g_rms, VERSION 3.3.1
Source code file: nrjac.c, line: 129

Fatal error:
Error: Too many iterations in routine JACOBI
I have searched in gmx archives regarding this problem , I found that mismatch 
between trjactory and reference structure file, but in my case both are matched 
atoms

Is there any mistake in either selecting options of making index file or I have 
given wrong option while using g_rms

Pls suggest me
Thanks in advance.___
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Re: [gmx-users] g_rms , getting rmsd matrix and the histogram of this matrix

[Xavier Periole]

On Tue, 12 Feb 2008 20:56:04 +0200
 "OZGE ENGIN" <[EMAIL PROTECTED]> wrote:
Hi all, 

I have three questions. 

1)In order to get the rmsd distribution of all the conformations, I used 
g_rmsd. In the help menu, it is stated that g_rmsd compares the structure 
given by -s and compares it to the others which are given by -f option. 
Consequently, I can not get the rmsd between all pairs of conformations. how 
can I get the rmsd between all of the pairs?


g_cluster can give you the distribution of the pairwise rmsd. I guess that
is what you are looking for.

2)How can I get the rmsd matrix? In manual, it is indicated that with option 
-m, you produce a matrix. However, with xv, I can not see the matrix exactly. 
3)Is there any specific tool for plotting the histogram of the rmsd matrix?


g_cluster



Thanks in advance

Ozge Engin
=
Computational Science & Engineering
Koc University
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-
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-
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[gmx-users] g_rms , getting rmsd matrix and the histogram of this matrix

[OZGE ENGIN]

Hi all,

I have three questions.

1)In order to get the rmsd distribution of all the conformations, I used 
g_rmsd. In the help menu, it is stated that g_rmsd compares the structure given 
by -s and compares it to the others which are given by -f option. Consequently, 
I can not get the rmsd between all pairs of conformations. how can I get the 
rmsd between all of the pairs?

2)How can I get the rmsd matrix? In manual, it is indicated that with option 
-m, you produce a matrix. However, with xv, I can not see the matrix exactly.
3)Is there any specific tool for plotting the histogram of the rmsd matrix?

Thanks in advance

Ozge Engin
=
Computational Science & Engineering
Koc University
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Re: [gmx-users] g_rms

[Mark Abraham]

andrea carotti wrote:

So does the -Rmat option not produce a human-readable text file?

Hi, unfortunately I can't see this option in g_rms.
I'm using the v 3.3.1 and also on the reference page online there is not
-Rmat. Am i missing something?


Hmm, you're right. Installations that I know are 3.3.1 don't have this 
-Rmat option, but the g_rms in the GROMACS installation on my desktop 
machine reports itself as 3.3.1 and has this -Rmat option. Probably, I'm 
still running a beta 3.3.1 (and since I don't use this for more than 
manual checking I've never bothered to update the version!) and this 
option never made it to the production version. I can't think of any way 
to check this, however. Do the developers know?


Please accept my apologies for the misunderstanding.

Mark
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Re: [gmx-users] g_rms

[andrea carotti]

> So does the -Rmat option not produce a human-readable text file?
Hi, unfortunately I can't see this option in g_rms.
I'm using the v 3.3.1 and also on the reference page online there is not
-Rmat. Am i missing something?
Thanks
Andrea


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Re: [gmx-users] g_rms

[Mark Abraham]

andrea carotti wrote:

Hi again,

If you read g_rms -h like I suggested last time, you'll see that -f2 and 
-s serve the same purpose with the former using a trajectory and the 
latter a single structure. That document doesn't say what happens when 
you use both... but the operation you're trying to do doesn't need both!

the -h option is my standard first step when i use all the gmx-tools and I've 
read and done it like every time.


So does the -Rmat option not produce a human-readable text file?

Mark
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Re: [gmx-users] g_rms

[andrea carotti]

Hi again,

> If you read g_rms -h like I suggested last time, you'll see that -f2 and 
> -s serve the same purpose with the former using a trajectory and the 
> latter a single structure. That document doesn't say what happens when 
> you use both... but the operation you're trying to do doesn't need both!
the -h option is my standard first step when i use all the gmx-tools and I've 
read and done it like every time.
I've tried to use -f2 option without using the -s and it comes out with the 
error "topol.tpr not found" so it's not "so optional", but it's needed also 
when using the -f2 option..
I've alsto tried to use the -s with my traj without using the -f2 option but it 
creates a matrix 2200x2200.
However the problem still remain unsolved or misunderstanded.
If i use the my only working command line
g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin 

I obtain a rmsd.xvg with 2 columns. So, which is the meaning of that value? a 
mean of all the rmsd calculated for that frame in respect to the other 33 refs?
Thanks
Andrea

-- 

Andrea Carotti
Dipartimento di Chimica e Tecnologia del Farmaco
Via del Liceo, 1
06123 Perugia, Italy
phone: +39 075 585 5169
fax: +39 075 585 5161
www http://rpg.unipg.it
personal www http://iris.chimfarm.unipg.it/users/andcar

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Re: [gmx-users] g_rms

[Mark Abraham]

andrea carotti wrote:

Hi,
You should be getting such a 2200x33 matrix. My guess is that the 
command line or files that you're using are not what you think they

are :-)
my command line is 

g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin 


If you read g_rms -h like I suggested last time, you'll see that -f2 and 
-s serve the same purpose with the former using a trajectory and the 
latter a single structure. That document doesn't say what happens when 
you use both... but the operation you're trying to do doesn't need both!



Note that the pdbs (traj and ref) have the same number of atoms (same
structure).
During the calculation i can see that it is creating the 2200x33 matrix,
but on the rmsd.xvg i find only two columns. From the xpm and dat files
i can't extract the matrix (i don't know) to a text file.


There's an option to g_rms that writes a text matrix for importing into 
R. Look it up.


Mark
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Re: [gmx-users] g_rms

[andrea carotti]

Hi,
> You should be getting such a 2200x33 matrix. My guess is that the 
> command line or files that you're using are not what you think they
> are :-)
my command line is 

g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin 

Note that the pdbs (traj and ref) have the same number of atoms (same
structure).
During the calculation i can see that it is creating the 2200x33 matrix,
but on the rmsd.xvg i find only two columns. From the xpm and dat files
i can't extract the matrix (i don't know) to a text file.
I hope this could clarify better my question
Thanks
Andrea



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Re: [gmx-users] g_rms

[Mark Abraham]

andrea carotti wrote:

Hi and thanks for answering to my previous question.
Now I'm calculating the rmsd between two trajectories (-f2 option).
One is made by 2200 frames and the other has 33 frames..Now I've some
doubt about the output (rmsd.xvg), cause this file has only two columns
with 2200 rows ...i was imaging that it should have 2200 rows and 33
columns, am I wrong? 


You should be getting such a 2200x33 matrix. My guess is that the 
command line or files that you're using are not what you think they are :-)



The second question is something that is already been asked before..it
could be usefull to obtain the matrix 2200 x 33 in a human readable
file. Is it possible without hacking the code? Perhaps using external
scripts? 


There's a human readable matrix form that can already be written. Check 
out g_rms -h


Mark
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[gmx-users] g_rms

[andrea carotti]

Hi and thanks for answering to my previous question.
Now I'm calculating the rmsd between two trajectories (-f2 option).
One is made by 2200 frames and the other has 33 frames..Now I've some
doubt about the output (rmsd.xvg), cause this file has only two columns
with 2200 rows ...i was imaging that it should have 2200 rows and 33
columns, am I wrong? 
The second question is something that is already been asked before..it
could be usefull to obtain the matrix 2200 x 33 in a human readable
file. Is it possible without hacking the code? Perhaps using external
scripts? 
Thanks a lot again
Andrea

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Re: [gmx-users] g_rms: fitting to one residue whilst measuring rmsd of another

[Tsjerk Wassenaar]

Hi Jo,

You're using 3.2.1? The first query is for the group to use for
fitting, then you're asked for how many groups you want the RMSD and
subsequently asked to give the groups. So the RMSD you get for
resid162 is probably what you want.

With version 3.3.1 you can also fit the trajectory using trjconv and
use g_rms with the option -fit none, in which case it will only ask
for one group to determine the RMSD for.

Hope it helps,

Tsjerk

On 8/27/07, jo hanna <[EMAIL PROTECTED]> wrote:
> Hi
>
> What I want to do is to calculate the RMSD of one binding pocket residue of
> my protein after fitting to the Ligand in my simulation.
>
> I have tried the following using g_rms:
>
>  selecting 12 LIG
> groups to compare 2
> selecting 12 LIG
>  selecting 16 resid162
>
> But I don't know if this is the doing the correct thing, or if this is the
> correct way to do this.
> Could anyone please advise?
>
> Thanks
> Jo
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] g_rms: fitting to one residue whilst measuring rmsd of another

[jo hanna]

Hi

What I want to do is to calculate the RMSD of one binding pocket residue of
my protein after fitting to the Ligand in my simulation.

I have tried the following using g_rms:

selecting 12 LIG
groups to compare 2
selecting 12 LIG
selecting 16 resid162

But I don't know if this is the doing the correct thing, or if this is the
correct way to do this.
Could anyone please advise?

Thanks
Jo
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Re: [gmx-users] g_rms recognition of xtc files

[Mark Abraham]

Beevers, Andrew wrote:


Dear All

I am trying to process xtc files from an MD simulation to produce an 
RMSD trace. However I am confronted with the following message:


fatal error: file filename.xtc not found.

These files are present and some have been processed before in the same 
way without this problem.


The amount of used memory has increased since this time, could this be a 
factor?


That wouldn't result in this error.

Check with ls -l and pwd where the files and you really are.

Mark
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[gmx-users] g_rms recognition of xtc files

[Beevers, Andrew]

Dear All

I am trying to process xtc files from an MD simulation to produce an RMSD 
trace. However I am confronted with the following message:

fatal error: file filename.xtc not found.

These files are present and some have been processed before in the same way 
without this problem.

The amount of used memory has increased since this time, could this be a factor?

Thank you in advance

Dr Andy Beevers
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Re: [gmx-users] g_rms v. g_rmsdist

[Tsjerk Wassenaar]

Hi Gleb,

g_rmsdist calculates a matrix of interatomic distances, averages these
and calculates the average deviation from the average. g_rms
superimposes two structures (superimposes the averages) and calculates
the average deviation over the pairs of equal atoms in the structures.

Hope I am clear enough...

Best,

Tsjerk

On 3/15/07, Gleb Solomentsev <[EMAIL PROTECTED]> wrote:


 Hello,

 I am trying to figure out what the difference between these two
applications is. The calculation is of the RMSD for a protein unfolding
trajectory and I get different results with g_rms and g_rmsdist. I have
looked at the manual and all I can find is that:

 "g_rmsdist computes the root mean square deviation of atom distances, which
has the advantage that no fit is needed like in standard RMS deviation as
computed by g_rms."

 What fit is this referring to and would this be the source of my
differences?

 I am getting larger RMSD values using g_rms.

 Thanks,
 Gleb



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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] g_rms v. g_rmsdist

[Gleb Solomentsev]

Hello,

I am trying to figure out what the difference between these two 
applications is. The calculation is of the RMSD for a protein unfolding 
trajectory and I get different results with g_rms and g_rmsdist. I have 
looked at the manual and all I can find is that:


"g_rmsdist computes the root mean square deviation of atom distances, 
which has the advantage that no fit is needed like in standard RMS 
deviation as computed by g_rms 
."


What fit is this referring to and would this be the source of my 
differences?


I am getting larger RMSD values using g_rms.

Thanks,
Gleb


begin:vcard
fn:Gleb Solomentsev
n:Solomentsev;Gleb
org:University College of Dublin;Chemical and Bioprocess Engineering
adr:;;UCD Belfield;Dublin;;4;Ireland
email;internet:[EMAIL PROTECTED]
title:PhD Student
tel;work:+353 1 716 1691
version:2.1
end:vcard

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Re: [gmx-users] g_rms, least square fit

[Mark Abraham]

kanin wichapong wrote:

Dear All,
   I have some questions about g_rms. When I start to calculate the 
rmsd using g_rms first I will get "Select group for least squares fit" 
and then "Select group for RMSD calculation", does both two times need 
to be the same group or not? 


You can fit based on one group of atoms, and then compare the fit based 
on another group of atoms.


Like in my case, I want to calculate rmsd 
of one residue of the inhibitor which is tetrapeptide. What should be 
selected for the least square fit, Backbone of protein, all residue of 
inhibitor group or the group of the residue that I want to calculate the 
rmsd?


Pick something you think should make a constant reference frame and use 
that for the fitting. Then use the group you think should vary for the 
RMSD calculation. Or just play with it and see.


Mark
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[gmx-users] g_rms, least square fit

[kanin wichapong]

Dear All,   I have some questions about g_rms. When I start to calculate the rmsd using g_rms first I will get "Select group for least squares fit" and then "Select group for RMSD calculation", does both two times need to be the same group or not? Like in my case, I want to calculate rmsd of one residue of the inhibitor which is tetrapeptide. What should be selected for the least square fit, Backbone of protein, all residue of inhibitor group or the group of the residue that I want to calculate the rmsd? 
  Thank you so much in advance for all of your help.With Best Regard,Kanin
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Re: [gmx-users] g_rms, matrix and raw data

[Tsjerk Wassenaar]

Hi Ninoo,

You can hack the code of gmx_rms.c in [GMXSRCDIR]/src/tools/ to output
the matrix generated into a human readable format. It is also possible
to write a raw binary file which can easily be processed using a
scripting language such as python (use g_rms -bin).

Best,

Tsjerk

On 9/27/06, ninoo mani <[EMAIL PROTECTED]> wrote:

Dear Mark
I read the manual but I could not find any option to
get the original values of the matrix. I will be
highly appreciative if you can help.
thanks
Ninoo Mani


--- Mark Abraham <[EMAIL PROTECTED]> wrote:

> > Dear all
> >
> > I run g_rms with -m option that produces a matrix
> in
> > .xpm format. Is it possible somehow to obtain raw
> data
> > i.e. the real numerical values of the elements of
> the
> > matrix?
>
> man g_rms
>
> Mark
>
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--
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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Re: [gmx-users] g_rms, matrix and raw data

[ninoo mani]

Dear Mark
I read the manual but I could not find any option to
get the original values of the matrix. I will be
highly appreciative if you can help.
thanks
Ninoo Mani


--- Mark Abraham <[EMAIL PROTECTED]> wrote:

> > Dear all
> >
> > I run g_rms with -m option that produces a matrix
> in
> > .xpm format. Is it possible somehow to obtain raw
> data
> > i.e. the real numerical values of the elements of
> the
> > matrix?
> 
> man g_rms
> 
> Mark
> 
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Re: [gmx-users] g_rms, matrix and raw data

[Mark Abraham]

> Dear all
>
> I run g_rms with -m option that produces a matrix in
> .xpm format. Is it possible somehow to obtain raw data
> i.e. the real numerical values of the elements of the
> matrix?

man g_rms

Mark

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[gmx-users] g_rms, matrix and raw data

[ninoo mani]

Dear all

I run g_rms with -m option that produces a matrix in
.xpm format. Is it possible somehow to obtain raw data
i.e. the real numerical values of the elements of the
matrix?
Thanking in advance,
Ninoo



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