Hi,
I' like to know if it is possible to get the average RMSD through g_rms
command? Or I need to get it manually?
Thanks for your suggestions.
Sincerely,
Shima
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On 5/5/13 12:40 PM, Shima Arasteh wrote:
Hi,
I' like to know if it is possible to get the average RMSD through g_rms
command? Or I need to get it manually?
Use g_analyze.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of
Average coordinates are problematic and not generally representative. Consider
for instance the average coordinates of a methyl group connected to X. The
rotation around the C-X bond causes the average positions of the hydrogens to
line up. Consider using g_cluster to find representative
Dear Sir,
Thanks for the useful insight.
On Fri, Apr 26, 2013 at 2:21 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Average coordinates are problematic and not generally representative.
Consider for instance the average coordinates of a methyl group connected
to X. The rotation around the
Hi Bipin Singh,
That indeed gives you the RMSD against the average. Do think about it a bit
more: do you want the average of the whole structure, or should you account
for a phase of relaxation?
Cheers,
Tsjerk
On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul jalem...@vt.edu wrote:
On
Thanks for your reply.
Actually I am interested to see how much structural deviation is occurring
in a protein during the simulation from its average position of atoms
rather than the initial position (crystal structure or starting structure).
The motivation of doing this analysis is the fact that
Hi all,
Please let me know whether this is the right way to calculate RMSD from the
average structure from a simulation:
g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
average.pdb: is the pdb file produced using -ox option of g_rmsf.
--
*---
Thanks and Regards,
Bipin
On 4/24/13 3:06 AM, bipin singh wrote:
Hi all,
Please let me know whether this is the right way to calculate RMSD from the
average structure from a simulation:
g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
average.pdb: is the pdb file produced using -ox option of g_rmsf.
You can
, January 24, 2013 8:54 PM
Subject: Re: [gmx-users] RMSD
you can make a simple script which calculates all the pairwise
RMSD
values with g_rms. By doing this you can make a RMSD matrix.
I think you can get the RMSD matrix from g_cluster in one go.
The usefulness of this depends on what
Enviado: miércoles, 23 de enero de 2013 16:14
Asunto: Re: [gmx-users] RMSD
What I see in xvg file is as below:
# g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg
#
# g_rms is part of G R O M A C S:
#
# Gromacs Runs On Most of All Computer Systems
#
@ title RMSD
@ xaxis label Time (ps)
@ yaxis
Arasteh shima_arasteh2...@yahoo.com
Para: Discussion list for GROMACS users gmx-users@gromacs.org
Enviado: miércoles, 23 de enero de 2013 16:14
Asunto: Re: [gmx-users] RMSD
What I see in xvg file is as below:
# g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg
#
# g_rms is part of G R O M A C S
my purposed conformers?
Thanks for all your suggestions.
Sincerely,
Shima
From: Leandro Bortot leandro@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thursday, January 24, 2013 8:54 PM
Subject: Re: [gmx-users] RMSD
you
Hi,
Is it possible to get RMSD of 10 different pdb files by GROMACS?
g_rms may help?
Sincerely,
Shima
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On 1/23/13 10:38 AM, Shima Arasteh wrote:
Hi,
Is it possible to get RMSD of 10 different pdb files by GROMACS?
Relative to what? Each other? Some universal reference?
g_rms may help?
That, or g_confrms, depending on what you're actually trying to measure.
-Justin
--
I think what you really need is not Gromacs.
For example, you can use UCSF Chimera to get alignment and RMSD between two
PDBs.
dawei
On Wed, Jan 23, 2013 at 10:38 AM, Shima Arasteh shima_arasteh2...@yahoo.com
wrote:
Hi,
Is it possible to get RMSD of 10 different pdb files by GROMACS?
-users] RMSD
On 1/23/13 10:38 AM, Shima Arasteh wrote:
Hi,
Is it possible to get RMSD of 10 different pdb files by GROMACS?
Relative to what? Each other? Some universal reference?
g_rms may help?
That, or g_confrms, depending on what you're actually trying to measure.
-Justin
On 1/23/13 12:48 PM, Shima Arasteh wrote:
I want to find the structure with the lowest RMSD, so I think it does not make
different to set any of pdb files as the ref structure.
I made an attempt and got the RMSD regarding the first pdb file. The RMSD
relative to -1 for the ref structure, is
for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Wednesday, January 23, 2013 9:36 PM
Subject: Re: [gmx-users] RMSD
On 1/23/13 12:48 PM, Shima Arasteh wrote:
I want to find the structure with the lowest RMSD, so I think it does not
make different to set any of pdb files as the ref structure
On 1/23/13 1:14 PM, Shima Arasteh wrote:
What I see in xvg file is as below:
# g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg
#
# g_rms is part of G R O M A C S:
#
# Gromacs Runs On Most of All Computer Systems
#
@title RMSD
@xaxis label Time (ps)
@yaxis label RMSD (nm)
@TYPE xy
@
Dear Mark,
Thanks for the reply.
But one thing I am just wondering is that while calculating the RMSD,
I'm considering the backbone only. So I can take the initial pdb file
as reference for the trajectory. While doing so I see the RMSD graph
is continuing to increase and not getting equilibrium
On 30/07/2012 4:49 PM, tarak karmakar wrote:
Dear Mark,
Thanks for the reply.
But one thing I am just wondering is that while calculating the RMSD,
I'm considering the backbone only. So I can take the initial pdb file
as reference for the trajectory. While doing so I see the RMSD graph
is
Dear All,
In my initial protein pdb structure I have added some external ligand
molecules and as a result of that there are several short contacts.
So, well, I minimized the system and then got the 'prot_min.gro' file.
Now after the equilibration run, I plotted the RMSD of the resulting
On 30/07/2012 3:39 AM, tarak karmakar wrote:
Dear All,
In my initial protein pdb structure I have added some external ligand
molecules and as a result of that there are several short contacts.
So, well, I minimized the system and then got the 'prot_min.gro' file.
Now after the equilibration
Dear All,
During a 1 ns production analysis (before it completes), I can analysis the
RMSD by g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns without
influence the normal calculation of the production analysis, right?
Cheers,
Acoot --
gmx-users mailing list
Acoot Brett wrote:
Dear All,
During a 1 ns production analysis (before it completes), I can analysis
the RMSD by g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns
without influence the normal calculation of the production analysis, right?
It's always safer to make a copy of
Hi Davide,
If you've checked the trajectory, and you've assured that there are no
atoms wrapping over the periodic boundaries, and you've noticed a
sudden change in conformation, then probably that's what it is: a
sudden change in conformation. That does agree with the plot. After a
rather
Hi Tsjerk,
thanks very much for your prompt reply.
I checked the last 5ns rmsd against an average structure calculated in the
same time range and effectively the system seems to be converging (I
attached the graph).
However, the switch seems unlikely as the protein seems to lose part of its
Sorry I realized I attached the .xvg.
Here is a png for a easier visualization. Sorry for the inconvenience.
Thanks,
Davide
2012/3/14 Davide Mercadante dmer...@aucklanduni.ac.nz
Hi Tsjerk,
thanks very much for your prompt reply.
I checked the last 5ns rmsd against an average structure
Dear gromacs users,
I have performed ~30ns MD on a protein in TIP4P water using the OPLS
forcefield.
I have concatenated the trajectories for each step using trjcat and removed
pbc effects using pbc nojump.
All the particles of the system now don't jump anymore and the molecule
doesn't appear as
Hi GROMACS Users,
I have simulated a protein(pdb id 3D9S)
for 5 nanoseconds. This protein contains 978 residues and after 5
nanoseconds I got 2.35 by comparing pdb structure with simulated one. I
want to know is this value is ok or protein is disrupted?
Yours
On 9/01/2012 8:26 PM, madhumita das wrote:
Hi GROMACS Users,
I have simulated a protein(pdb id
3D9S) for 5 nanoseconds. This protein contains 978 residues and after
5 nanoseconds I got 2.35 by comparing pdb structure with simulated
one. I want to know is
10:18
Para: Discussion list for GROMACS usersgmx-users@gromacs.org
Asunto: Re: [gmx-users] RMSD
On 11/15/11 8:23 PM, shahid nayeem wrote:
Dear all
I am interested to get contour plot of residue RMSD vs time graph. I want
to get the flexible and rigid regions of protein chain during
Dear all
I am interested to get contour plot of residue RMSD vs time graph. I want
to get the flexible and rigid regions of protein chain during simulation.
g_rmsf does not gives me this plot.
Please help
shahid Nayeem
--
gmx-users mailing listgmx-users@gromacs.org
On 11/15/11 8:23 PM, shahid nayeem wrote:
Dear all
I am interested to get contour plot of residue RMSD vs time graph. I
want to get the flexible and rigid regions of protein chain during
simulation. g_rmsf does not gives me this plot.
Please help
shahid Nayeem
Try g_rmsf -res , it could
.
regards
Felipe
Mensaje original De: gianluca.sant...@ibs.fr Fecha: 15-nov-2011 10:18
Para: Discussion list for GROMACS usersgmx-users@gromacs.org Asunto: Re:
[gmx-users] RMSD On 11/15/11 8:23 PM, shahid nayeem wrote:
Dear all
I am interested to get contour plot of residue RMSD vs time
any hints? :(
03 Ekim 2011 22:32 tarihinde ahmet yıldırım ahmedo...@gmail.com yazdı:
I look at chapter 8 but I didnt found that I want. can you give a hint?
Thanks
2011/10/3 Mark Abraham mark.abra...@anu.edu.au
On 3/10/2011 10:29 PM, ahmet yıldırım wrote:
Dear users,
How can I
On 4/10/2011 7:05 PM, ahmet y?ld?r?m wrote:
any hints? :(
You didn't find something useful in the section titled Root mean square
deviations in structure?
Mark
03 Ekim 2011 22:32 tarihinde ahmet y?ld?r?m ahmedo...@gmail.com
mailto:ahmedo...@gmail.com yazd?:
I look at chapter 8 but
No, it calculates with respect to the positions atom. but I want to
calculate the RMSD bonds (A˚ ) and RMSD angles (o).
2011/10/4 Mark Abraham mark.abra...@anu.edu.au
On 4/10/2011 7:05 PM, ahmet yıldırım wrote:
any hints? :(
You didn't find something useful in the section titled Root mean
Hey :)
If that is what you want, you'll have to turn to programming. But what do
you think to gain from it? First get to the bottom of things you can do with
gromacs already. Then, if the tools available don't help in answering your
question, think of what you'd need to get it done.
Cheers,
Dear users,
How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)?
Thanks in advance
--
Ahmet YILDIRIM
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Please search the archive at
On 3/10/2011 10:29 PM, ahmet yıldırım wrote:
Dear users,
How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)?
Please start your search in chapter 8 of the manual, and consider doing
some tutorial material. Someone is likely to have covered some similar
procedures.
Mark
--
I look at chapter 8 but I didnt found that I want. can you give a hint?
Thanks
2011/10/3 Mark Abraham mark.abra...@anu.edu.au
On 3/10/2011 10:29 PM, ahmet yıldırım wrote:
Dear users,
How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)?
Please start your search in chapter 8 of
On 6/05/2011 2:21 AM, Sikandar Mashayak wrote:
Hi
As a test case, I did two simulations one the usual Protein in Water
and other with Vsites at COM of each monomer but these Vsites dont
interact with anyone else. I was expecting results of these two should
match almost exactly, but when I
On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote:
Hi
As a test case, I did two simulations one the usual Protein in Water and
other with Vsites at COM of each monomer but these Vsites dont interact with
anyone else. I was expecting results of these two should match almost
exactly,
well the deviations are about more than 0.5 nm..
On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai p...@uab.edu wrote:
On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote:
Hi
As a test case, I did two simulations one the usual Protein in Water and
other with Vsites at COM of each monomer
On 6/05/2011 5:32 PM, Sikandar Mashayak wrote:
well the deviations are about more than 0.5 nm..
And what does gmxcheck -s1 -s2 show?
Mark
On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai p...@uab.edu
mailto:p...@uab.edu wrote:
On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote:
Hi
As a test case, I did two simulations one the usual Protein in Water and
other with Vsites at COM of each monomer but these Vsites dont interact with
anyone else. I was expecting results of these two should match almost
exactly, but when I compare the rmsd for Protein there seems to be
Hey :)
You probably want to fit on the protein and calculate the RMSD on the
ligand. You may need to specify these groups in an index file.
Hope it helps,
Tsjerk
On Mar 27, 2011 3:28 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Nancy wrote: Hi All, I need to determine the RMSD of a small
Hi All,
I need to determine the RMSD of a small molecule cocrystallized ligand,
against a large number of predicted docked conformations. Please let me
know what is the best method for doing this.
Thank you very much,
Nancy
--
gmx-users mailing listgmx-users@gromacs.org
Nancy wrote:
Hi All,
I need to determine the RMSD of a small molecule cocrystallized ligand,
against a large number of predicted docked conformations. Please let me
know what is the best method for doing this.
I answered this yesterday:
Hi Mark,
Thanks for your feedback. The simulations are running now again.
I got one questions, I think it will be also of interest for the
others on the mailinglist.
I used grompp with the -t state0.cpt option, are the starting
velocities taken from the cpt files or are the assigned randomly
Henri Mone wrote:
Hi Mark,
Thanks for your feedback. The simulations are running now again.
I got one questions, I think it will be also of interest for the
others on the mailinglist.
I used grompp with the -t state0.cpt option, are the starting
velocities taken from the cpt files or are the
Hi All, hi Mark,
Here are some more details. The outputs and error messages are
attached at the end of the e-mail. After truncation I get the error
message [1a], gromacs has problems with the checksum of the trr fles.
After truncation the trajectories (xtc, trr) have the same length of
27752
Dear Gromacs Users/ Experts and Beginners,
I'm using Gromacs 4.5.3 to run REMD simulation. The REMD simulations
stooped abruptly and therefore the replicas have uneven information.
One of the checkpoint differ in time and frame compared to other
replicas. My case is very similar to the problem
On 7/03/2011 8:23 PM, Henri Mone wrote:
Dear Gromacs Users/ Experts and Beginners,
I'm using Gromacs 4.5.3 to run REMD simulation. The REMD simulations
stooped abruptly and therefore the replicas have uneven information.
One of the checkpoint differ in time and frame compared to other
replicas.
Hi Ahmet,
I'm not sure whether it's been checked. It has been found that NMR
structures tend to yield larger deviations than crystal structures. If
you're going to try, due make sure to compensate for other potential
influences, such as the size and sphericity of the proteins.
Cheers,
Tsjerk
Hi,
Is there a relationship between RMSD value obtained from the calculation and
Resolution value in PDB file?
Thanks in advance
--
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| Tel: +61 3 9902 9376
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| E-mail: itamar.k...@med.monash.edu.au
- Original Message -
From: Anupam Nath Jha anu...@mbu.iisc.ernet.in
Date: Sunday, May 9, 2010 3:48 pm
Subject: [gmx-users] rmsd between different
Anupam Nath Jha wrote:
Dear all
I made an index file with 4 different groups for 4 different chains (since my
protein is a tetramer) and then run
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
to get the rmsd between two different monomers from the same structure,
it asked me two
Itamar Kass wrote:
Hi Anupam ,
To me it seems that you have used the the wrong groups for the RMSD, you
actually compare the protein to himself. Have a second look on at the
group contact, you groups should be numbered 12 or higher.
Not in this case. The headers of the .xvg file in the
Anupam Nath Jha wrote:
Dear all
I made an index file with 4 different groups for 4 different chains (since my
protein is a tetramer) and then run
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
to get the rmsd between two different monomers from the same structure,
it asked me
Anupam Nath Jha wrote:
Anupam Nath Jha wrote:
Dear all
I made an index file with 4 different groups for 4 different chains (since my
protein is a tetramer) and then run
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
to get the rmsd between two different monomers from the same
On 9/05/2010 9:29 PM, Justin A. Lemkul wrote:
Anupam Nath Jha wrote:
Anupam Nath Jha wrote:
Dear all
I made an index file with 4 different groups for 4 different chains
(since my
protein is a tetramer) and then run
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
to get the rmsd
Ok.
But when I run this command
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
it ask me groups... and that i thought is for fitting///
for example -
Select group for least squares fit
Group 0 (C-alpha_chain1) has 249 elements
Group 1
you said you have used online server for superimposition ...
which one you used...
try TOPMATCH server
On Sun, May 9, 2010 at 5:31 PM, Anupam Nath Jha anu...@mbu.iisc.ernet.inwrote:
Ok.
But when I run this command
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
it ask me
On 9/05/2010 10:01 PM, Anupam Nath Jha wrote:
Ok.
But when I run this command
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
it ask me groups... and that i thought is for fitting///
for example -
Select group for least squares fit
Group 0
Dear all
I made an index file with 4 different groups for 4 different chains (since my
protein is a tetramer) and then run
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
to get the rmsd between two different monomers from the same structure,
it asked me two different groups and I gave
Dear all
How can we calculate the rmsd between different monomers from of a protein. for
example I have a tetramer and I have to calculate the rmsd between chain A to B,
A to C and A to D with time.
I was trying using g_rms but couldn't do that.
thanks with regards
anupam
--
Science is
There is one web-server in our lab.
http://10.188.1.15/3dss/
Use third option.
On Fri, May 7, 2010 at 2:41 PM, Anupam Nath Jha anu...@mbu.iisc.ernet.inwrote:
Dear all
How can we calculate the rmsd between different monomers from of a protein.
for
example I have a tetramer and I have to
On 7/05/2010 7:11 PM, Anupam Nath Jha wrote:
Dear all
How can we calculate the rmsd between different monomers from of a protein. for
example I have a tetramer and I have to calculate the rmsd between chain A to B,
A to C and A to D with time.
I was trying using g_rms but couldn't do that.
g_confrms -f1 conf1.gro -f2 conf2.gro -n1 ind1.ndx -n2 ind2,ndx should
do the trick.
On Feb 9, 2010, at 1:27 AM, Mark Abraham wrote:
On 09/02/10 10:20, V Hariharan wrote:
Hello All,
I've taken the average peptide structure from two different MD
simulations using g_rmsf. Is there a
Hello All,
I've taken the average peptide structure from two different MD simulations
using g_rmsf. Is there a method for calculating the RMSD between those two
structures? The only difference between the two peptides is a single residue
mutation. Thanks.
--Venk
On 09/02/10 10:20, V Hariharan wrote:
Hello All,
I've taken the average peptide structure from two different MD
simulations using g_rmsf. Is there a method for calculating the RMSD
between those two structures? The only difference between the two
peptides is a single residue mutation. Thanks.
Hello there,
I have used g_rms and g_cluster for RNA structure analysis and noticed that
they give me different rmsd values.
For example, calculating rmsd values using the g_rms gives me a minimum rmsd
value of 0.7nm, but using g_cluster
it gives me the minimum rmsd value of 0.3nm. Both uses
Segun Jung wrote:
Hello there,
I have used g_rms and g_cluster for RNA structure analysis and noticed
that they give me different rmsd values.
For example, calculating rmsd values using the g_rms gives me a minimum
rmsd value of 0.7nm, but using g_cluster
it gives me the minimum rmsd
Hi
I have 2 questions about rmsd calculation:
1) why rmsd calculation is done on heavy atoms?
2) what means of mass weighted superposition (rmsd is calculated after mass
weighted superposition)
Any help will highly appreciated!
--
gmx-users mailing listgmx-users@gromacs.org
leila karami wrote:
Hi
I have 2 questions about rmsd calculation:
1) why rmsd calculation is done on heavy atoms?
2) what means of mass weighted superposition (rmsd is calculated after
mass weighted superposition)
Consider the difference between centre of mass and center of geometry...
Dear friends,
I am able to plot, RMSD between Time (ps) by following command by using
GRACE..
g_rms -s md.tpr -f md.xtc
xmgrace rmsd.xvg
How we can I plot a graph betwwen RMSD and residue no ..??
My aim is to find RMSD at each residues. How i can do that?
looking forward for u r important
Hi, I'm trying to compare two proteins with the same number of aminoacids
with g_confrms, and it works all right, but it gives me the RMSD of the hole
protein, and I need the distances (or deviations) of each aminoacid. I know
this data shoul be there, but I don't know how to get it (I've got the
Andy Torres wrote:
Hi, I'm trying to compare two proteins with the same number of
aminoacids with g_confrms, and it works all right, but it gives me the
RMSD of the hole protein, and I need the distances (or deviations) of
each aminoacid. I know this data shoul be there, but I don't know how
Dear justin
I have rmsd graph from peptide (13 amino acid).would you please tell
me about generally range of rmsd for good simulation.In my table rmsd
start from 2 nm and come up to 3 and change between 3 to 3.5
nm.the solvent is tfe/water.thanks for your advise.
best regards
--
shahrbanoo karbalaee wrote:
Dear justin
I have rmsd graph from peptide (13 amino acid).would you please tell
me about generally range of rmsd for good simulation.In my table rmsd
start from 2 nm and come up to 3 and change between 3 to 3.5
nm.the solvent is tfe/water.thanks for your
tahnk you i'll try that
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Please don't post (un)subscribe requests to the
Hi,
i want to calculate rmsd on homologous protein structures that have different
residue numbers.
As far as i understood g_rms gives only rmsd of the same structure in different
configurations, but it doesn't fit homologous protein structures?
In Option -f2 can i provide a trajectory of a
Tatsiana Kirys wrote:
Hi,
i want to calculate rmsd on homologous protein structures that have different residue numbers.
As far as i understood g_rms gives only rmsd of the same structure in different configurations, but it doesn't fit homologous protein structures?
Yep.
In Option -f2 can
Hi,
For individual structures, you can use g_confrms.
If you want a trajectory you can download do_multiprot from the user
contributions section, and follow the instructions there. Note that
multiprot aligns based on the structure only (no sequence information).
Ran.
Tatsiana Kirys wrote:
Hi,
ravi sharma wrote:
Hello everyone
is there any idea how can i calculate rmsd for a given helix or all
helix in a protein from a trejectory???
Create an index group, specifying only the residues you care to analyze, and
pass it to g_rms.
-Justin
-Ravi
Ravi Datta Sharma
Lecturer,
Hi users,
I have run two systems of protein simulation for 7ns, the difference between
these systems change in the few resdues. After that I have done RMSD analysis.
When I superimposed these two 7ns protein simulation systems with crystal
structure seperately,I noticed that in one
On Sat, 9 Aug 2008, jayant james wrote:
hi !
I am interested in plotting the RMSD between two amino acids to see if
they come close or move away during simulations.
Any suggestions would be helpful.
g_mindist
Thanks
Jayant James
--
Jayasundar Jayant James
hi !
I am interested in plotting the RMSD between two amino acids to see if they
come close or move away during simulations.
Any suggestions would be helpful.
Thanks
Jayant James
--
Jayasundar Jayant James
www.chick.com/reading/tracts/0096/0096_01.asp)
Dear Users,
I've created two different models of the same
transmembrane protein. These two models were
created using homology approach using two different
templates (both with similar sequence similarity
to the sequence of the target protein). Next, I
did two separate 25ns simulations of
Hi Michael,
g_rms should do the trick. First create an index file having
an atom group identical in both systems. Then,
g_rms -s ref.pdb -f1 trj1.xtc -f2 trj2.xtc -m rmsd.xpm gives
you an rmsd matrix with entry ij given by
RMSD[(frame i of trj1),(frame j oftrj2)]. The diagonal of that
matrix
On Thu, 26 Jun 2008 13:38:30 +0200
Michal Kolinski [EMAIL PROTECTED] wrote:
Dear Users,
The closest tool to your need is g_rms using the option -m, which
generates a matrix of rmsd between all pairs of conformations
present in the trajectory.
To compare the two trajectories you should
Quite likely, it is due to part of molecule moving out of box. Also,
the molecule could be of multiple chain.
So you need to find a way to put the whole molecule in one piece. Try
various options from trjconv -pbc. If it is DNA, a trick is to define
one chain as an index group and then center
Like Yang Ye said, molecule is likely out of the box (just fix PBC).
This also happens when you don't know how to continue a broken
simulation (check the WIKI on gmx website)
I had this PBC issue many times. What works over here to make things easier is:
Be sure that in the reference frame -s the
Dear All,
Please tell, what should I predict from this graph?
I can understand this is normal type of graph.
Sorry for inconvenience, but I want to ask some questions,
my this job crashed many time, because of power shut down and I had to
restart this again and again, I used
Anamika Awasthi wrote:
Dear All,
Please tell, what should I predict from this graph?
We can't tell from your graph what's happening because you haven't told
us how you generated it. It's also not our job to do so - it's yours.
You can go at look at your data at the points that have
Dear all,
I used Gromacs-3.3.1 to simulate a small protein in water.
I have used 2 and 16 CPUs to do the simulation respectively. But
I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs
simulation and 0.20 nm in the 16 CPUs one. Are these differences
reasonable?
In the 16 CPUs
DeChang Li wrote:
Dear all,
I used Gromacs-3.3.1 to simulate a small protein in water.
I have used 2 and 16 CPUs to do the simulation respectively. But
I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs
simulation and 0.20 nm in the 16 CPUs one. Are these differences
Hi all,
There are two options for the -dista option of the g_cluster: rmsd of distance
and RMS deviation.
What is the difference between these two?
One of them gives the absolute rmsd of each frame and the other gives the
relative rmsd according to the average rmsd?
Thank you
Ozge Engin
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