On 4/25/13 10:12 AM, Vivek Modi wrote:
Hello,
I am using g_rmsf for analysis of a protein simulation. I want to calculate
the fluctuations with respect to a reference structure (using -od option).
But I am encountering a problem. Please correct me if I am wrong at some
place. The following two
Hello,
I am using g_rmsf for analysis of a protein simulation. I want to calculate
the fluctuations with respect to a reference structure (using -od option).
But I am encountering a problem. Please correct me if I am wrong at some
place. The following two methods are giving me different results. I
Hi Efrat,
2011/5/3 Efrat Noy :
> Hi,
>
> I have 2 questions regarding root mean square fluctuation calculations:
>
> 1. what exactly is the difference between the values in the rmsf.xvg file
> and the values in the rmsdev.xvg file (obtained with the -od option)? Are
> the rmsf.xvg values are stand
Hi,
I have 2 questions regarding root mean square fluctuation calculations:
1. what exactly is the difference between the values in the rmsf.xvg file and
the values in the rmsdev.xvg file (obtained with the -od option)? Are the
rmsf.xvg values are standard deviations of atom positions along the
Hi,
I am just curious that in the MD community whether there is consensus on how to
compare calculated rmsfs and expermental b-factors in x-ray. Should we use
average value per residue or one particular atom in a residue for comparsion.
Secondly, in NMR, people minimize a number of final calcula
Thanks a lot.
Valerio
"Justin A. Lemkul" ha scritto:
vferra...@units.it wrote:
Dear all,
I want to calculate the C-alfa fluctuation of a protein during a
trajectory with g_rmsf but I have just one question about the
otput: which is the difference using -o output and -od output? So
w
vferra...@units.it wrote:
Dear all,
I want to calculate the C-alfa fluctuation of a protein during a
trajectory with g_rmsf but I have just one question about the otput:
which is the difference using -o output and -od output? So what is the
difference between fluctuation and deviation?
ht
Dear all,
I want to calculate the C-alfa fluctuation of a protein during a
trajectory with g_rmsf but I have just one question about the otput:
which is the difference using -o output and -od output? So what is the
difference between fluctuation and deviation?
Thanks a lot in advance.
Va
Hi,
The reference is used for fitting. The RMSF is calculated with respect
to the average (fitted) structure, unless you explicitly specify that
deviations from the reference should be used.
Cheers,
Tsjerk
On Wed, Feb 16, 2011 at 7:08 AM, Mark Abraham wrote:
> On 16/02/2011 3:44 PM, kulleperum
On 16/02/2011 3:44 PM, kulleperuma.kulleper...@utoronto.ca wrote:
Dear all,
I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the
C-atoms with reference to the average structure between 5-10 ns of a
total of 10 ns simulation as below;
g_rmsf ?f md.xtc ?s md.tpr ?b 5000 ?e 1
Dear all,
I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the
C-atoms with reference to the average structure between 5-10 ns of a
total of 10 ns simulation as below;
g_rmsf ?f md.xtc ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg
My understanding of the RMSF is as follows;
RMSF
Original Message -
> From: Chih-Ying Lin
> Date: Tuesday, October 26, 2010 15:55
> Subject: [gmx-users] g_rmsf => average over # of time frames ???
> To: gmx-users@gromacs.org
>
>>
>>
>> Hi
>>
>> From source code => gmx_rmsf.c
&g
, October 26, 2010 15:55
Subject: [gmx-users] g_rmsf => average over # of time frames ???
To: gmx-users@gromacs.org
>
>
> Hi >
> From source code => gmx_rmsf.c > "g_rmsf computes the root mean square
> fluctuation (RMSF, i.e. standard ",
> "deviatio
Hi
>From source code => gmx_rmsf.c
"g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard ",
"deviation) of atomic positions ",
if (devfn) {
/* Calculate RMS Deviation */
for(i=0;(i--
gmx-users mailing listgmx-users@gromacs.org
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Chih-Ying Lin wrote:
Hi
g_rmsf -res yes ?
g_rmsf -res no ?
should I type "yes" to activate the "average-function"?
No. The command is either g_rmsf or g_rmsf -res. There is no "yes" or "no"
required.
As i tested "g_rmsf -res",
the average is not over time and not over the atoms
Hi
g_rmsf -res yes ?
g_rmsf -res no ?
should I type "yes" to activate the "average-function"?
As i tested "g_rmsf -res",
the average is not over time and not over the atoms in the residue.
Anyway, how to activate the "average function" ?
Thank you
Lin
Chih-Ying Lin wrote:
>
>
>
>
> Hi
> g
Chih-Ying Lin wrote:
Hi
From Manual
http://manual.gromacs.org/current/online/g_rmsf.html
g_rmsf =>
optiontypedefaultdescription
-[no]res bool noCalculate averages for each
residue
what does this function wor
Hi
>From Manual
http://manual.gromacs.org/current/online/g_rmsf.html
g_rmsf =>
optiontypedefaultdescription
-[no]res bool noCalculate averages for each
residue
what does this function work?
Thank you
Lin
--
gmx-users mailing listgmx-use
Chih-Ying Lin wrote:
Hi
g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg
From manual => it says " Calculate averages for each residue "
=> does Gromacs do average over time for each
residue ?
The average is done over time and over the atoms in the residue.
Hi
g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg
From manual => it says " Calculate averages for each residue "
=> does Gromacs do average over time for each residue
?
=> however, the results did not show difference with
and without " -res "
Hi Lin,
How many residues do you have and how many points do you get? (Only answer
for yourself). We're no substitute for your brain, you know...
Cheers,
Tsjerk
On Oct 25, 2010 7:47 AM, "Chih-Ying Lin" wrote:
Hi
g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg
*-[no]res*
bool
no
Calc
Hi
g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg
*-[no]res*
bool
no
Calculate averages for each residue
abcrmsf.xvg => average over time for each residue?
Thank you
Lin
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Please sea
Hi Pooja,
Try to get a grip on the file types and what they contain. A .cpt file
is a checkpoint file containing a single configuration. Not much
fluctuation to expect there. This sort of analysis only makes sense
for a trajectory, or at least an ensemble of structures. Try the .xtc
or the .trr fi
Hi,
I am running an npt simulation for a protein in water. For more than 50% of
the residues the backbone atoms have been restrained by applying
posrestraints. I ran g_rmsf to check if the pos-restraints were working
well. When I do this selecting 'backbone' from the groups menu, my rmsf file
give
Please does anyone know how is calculated the B factor in gromacs? What is
the formula that gives the B factor with the average coordinates with
g_rmsf?
Carla
On Fri, Jun 11, 2010 at 10:53 AM, Erik Marklund wrote:
> Hi,
>
> yes it can be done with g_covar, but such an average structure is often
Hi,
yes it can be done with g_covar, but such an average structure is often
of little physical significace. Imagine for instance the acerage
structure of a rotating methyle group (it's a bunch of atoms on a line).
Erik
Carla Jamous skrev:
Hi Tsjerk,
thank you for your answer.
Actually, for
Hi Tsjerk,
thank you for your answer.
Actually, for the initial structure, I took the values of the B factor, and
calculated the mean square displacement per atom. This is what I meant by
saying RMSF of initial structure. Anyway, thanks for the explanation.
But I have another question: I need to
Hi Carla,
On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous wrote:
> Hi Everyone,
>
> please I have a question concerning g_rmsf.
> I need to compare the RMSF from my initial structure to the RMSF of my
> average structure.
Single structures (initial c.q. average) do not have an RMSF.
> When I did
Hi Everyone,
please I have a question concerning g_rmsf.
I need to compare the RMSF from my initial structure to the RMSF of my
average structure.
To do so, I need to calculate the average per residue.
When I did
g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf
or
g_rmsf -s .tpr -f .xtc -n
Hi Tsjerk
Whether that's enough is largely dependent on the size of your protein
You should check whether you went beyond relaxation by inspecting the
cosine content of the first few eigenvectors.
This by itself does not mean anything. If it levels off at 0.1 nm,
okay, that's pretty good, but t
Hi Giordano,
> I agree that 10 ns
> are a short sampling but the total simulation time is 15 ns + 2 ns I
> used to reach 298K;
Whether that's enough is largely dependent on the size of your protein
You should check whether you went beyond relaxation by inspecting the
cosine content of the first f
Hi Tsjerk,
thanks for your reply.
I have inspected a trajectory
movie with vmd and made a superimposition of the starting and last
configuration with the reference structure (which is just the the
crystallographic pdb) and (inspecting them visually),
I do not see any significant conformational ch
Hi Giordano,
Do you have a conformational change? If you consider unidirectional
motion, in one or N coordinates alike, you would expect just what you
see for the fluctuations. In fact, it's not really fluctuation then.
10 ns is also pretty short for a simulation of a protein. It's likely
that you
Hi all,
I have the following problem: I have a simulation
of 10 ns of a protein in water. I have extracted the protein trajectory
with trjconv -pbc nojump and the fitted it to a reference structure
with trjconv -fit rot+trans.
If I run g_rmsf -nofit over two consecutive chunks of 5 ns i get very
sudheer babu wrote:
Hi,
I would like to calculate B-factor of protein, so I performed
command like this
g_rmsf -f .xtc -s .tpr -res -o fluctuate.xvg -od devi.xvg it has
run without error.Now i am bit doubting that which .xvg file have to
take for plot B-factor values?
I think
Hi,
I would like to calculate B-factor of protein, so I performed command
like this
g_rmsf -f .xtc -s .tpr -res -o fluctuate.xvg -od devi.xvg it has run
without error.Now i am bit doubting that which .xvg file have to take for
plot B-factor values?
B-factor is nothing but thermal devat
SWAPNA wrote:
Dear gmx users,
I have a basic query.
With respect to which structure are the rmsf values calculated per each
atom?
is it w.r.t average structure of the protein or the reference structure
that we provide using -s option?
I dont find any explanation of the output generated usi
Dear gmx users,
I have a basic query.
With respect to which structure are the rmsf values calculated per each
atom?
is it w.r.t average structure of the protein or the reference structure that
we provide using -s option?
I dont find any explanation of the output generated using g_rmsf. Please
ma
See http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
On Jan 4, 2008 11:20 AM, tangxuan <[EMAIL PROTECTED]> wrote:
> Thanks for your detailed explanation. Sorry for my words and I wrote
> them in a hurry without careful check. In fact, I can not see a whole
> protein in ref1.tpr and
Thanks for your detailed explanation. Sorry for my words and I wrote
them in a hurry without careful check. In fact, I can not see a whole
protein in ref1.tpr and part of subunits are out of box.
I do not know if this can be called jump.
Tang
Tsjerk Wassenaar wrote:
Hi Tang,
The subuni
Hi Tang,
The subunits have no contact each other obviously,
> without jump in them and I can not see an intact protein.
Please be more clear and try to write full, correct sentences. I suppose you
mean that the subunits are separated at start, so there has been a jump in
the setup stage.
Howeve
tangxuan wrote:
Hi Tsjerk,
Yes, you are right. My protein has multiple subunits. I have a original
tpr file ref1.tpr which is the input to start the simulation. I have
checked the protein structure
in this tpr file. The subunits have no contact each other obviously,
without jump in them and I
Hi Tsjerk,
Yes, you are right. My protein has multiple subunits. I have a original
tpr file ref1.tpr which is the input to start the simulation. I have
checked the protein structure
in this tpr file. The subunits have no contact each other obviously,
without jump in them and I can not see an i
Hi Tang,
It's just the general case of least-squares fitting:
1. Bring centres of geometry/mass to origin
2. Calculate (mass-weighted) rotation matrix
3. Rotate structure
(4. Calculate squared displacements)
But what do you mean with 'very different'. Can you provide an example? What
command lin
Hi,
Does anyone know how fitting step works in detail when running g_rmsf?
When I used two different tpr files with same protein structure but
different atoms position, the result is very different.
Can you explain this ?
many thanks!
Tang
___
gmx-
Tommy Carstensen wrote:
To the gmx-users,
When executing:
g_rmsf -f traj.trr -s topol.tpr -o rmsf.xvg -aniso
I get the following error after running through all the frames:
Segmentations fault
If I don't include the aniso flag I don't get an segfault. Can anyone
explain to me, why it is not wo
To the gmx-users,
When executing:
g_rmsf -f traj.trr -s topol.tpr -o rmsf.xvg -aniso
I get the following error after running through all the frames:
Segmentations fault
If I don't include the aniso flag I don't get an segfault. Can anyone
explain to me, why it is not working with the aniso flag?
I tried "trjconv -pbc nojump" to the whole protein and then calculated
the rmsf of the subunits. This method seems good to some separate
subunits, but other separate subunits still have strange high rmsf
values. I try "trjconv -pbc mol" too, and i have got same results. In
this simulation,the subu
tangxuan wrote:
Mark,thanks for your reply. I am not sure what happened and I can show
you the error message,"
Group 101 ( chK_chM) has 4070 elements
Group 102 ( chM_chO) has 4070 elements
Group 103 ( chO_chI) has 4070 elements
Group 104 ( chJ_chL) has 4070 elements
G
Mark,thanks for your reply. I am not sure what happened and I can show
you the error message,"
Group 101 ( chK_chM) has 4070 elements
Group 102 ( chM_chO) has 4070 elements
Group 103 ( chO_chI) has 4070 elements
Group 104 ( chJ_chL) has 4070 elements
Group 105 ( c
tangxuan wrote:
Dear all,
The protein I am working on is rubisco, consisting of 8 identical
large subunits and 8 identical small subunits. I try to calculate RMSF
for each large subunits, but the rmsf values seems much large to some
large subunits. So I check the first frame of the protein st
Dear all,
The protein I am working on is rubisco, consisting of 8 identical
large subunits and 8 identical small subunits. I try to calculate RMSF
for each large subunits, but the rmsf values seems much large to some
large subunits. So I check the first frame of the protein structutre,
and I fo
Arneh Babakhani wrote:
I see to calculate the average structure of a protein in a trajectory
minus any rotational + translational effects, using g_rmsf. Does the
-fit option (default yes) eliminate rot + trans contributions?
Yes, it will. If it can't rotate and translate, it's not much of a
I see to calculate the average structure of a protein in a trajectory
minus any rotational + translational effects, using g_rmsf. Does the
-fit option (default yes) eliminate rot + trans contributions?
Or must one use trjconv first, to convert the trajectory to some
reference frame eliminati
Hi all,
I was looking at the output of various g_rmsf runs, and came upon the fact that
the RMSF values obtained using -res and then choosing Mainchain (5)
for RMS calculation, were exactly the same as the RMSF values of
Mainchain Oxygen atoms obtained not using -res. I gave a look at the
code t
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