as i am very new to it.. can anyone suggest me how to change the graph format
obtained in gromacs (.xvg) into office 7 based system???
tyhanks in advance
-
thanks in advance :)
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Dear gmx users,
I am planning to run REMD for a peptide (406 atoms )+ solvent system
(27639). The temperature range I selected is from 300 to 500. I want to
select appropriate temp. for 56 replicas. I randomly chose some temp
distribution and the exchange probabilities was 0.0. I know that we can
Use Xmgrace or grace to convert .xvg to .jpeg format.
On Tue, Apr 23, 2013 at 12:32 AM, vansh vsha...@imtech.res.in wrote:
as i am very new to it.. can anyone suggest me how to change the graph
format
obtained in gromacs (.xvg) into office 7 based system???
tyhanks in advance
-
Dear Gromacs users,
a short disclaimer first: I'm new to using GROMACS and new to doing atomistic
resolution modelling. If I'm doing anything very wrong, I'd be very happy to
hear.
I'm trying to simulate ion current in a nanopore. My nanopore consists of LJ
particles positioned on the surface
hi..thanks for the reply..can you please write a command for it..
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thanks in advance :)
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Dear gmx users,
I am planning to run REMD for a peptide (406 atoms )+ solvent system
(27639). The temperature range I selected is from 300 to 500. I want to
select appropriate temp. for 56 replicas. I randomly chose some temp
distribution and the exchange probabilities was 0.0. I know that we can
Dear all,
I'm facing a problem when compiling Gromacs. This is the message I got:
numa_malloc.c:117:73: error: expected ‘)’ before ‘Processor’
numa_malloc.c:118:78: error: expected ‘)’ before ‘ProcNumber’
numa_malloc.c:121:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ be
It is there in every GROMACS manual or else you can even use xmgrace -h in
ur command prompt.
On Tue, Apr 23, 2013 at 1:41 AM, vansh vsha...@imtech.res.in wrote:
hi..thanks for the reply..can you please write a command for it..
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thanks in advance :)
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View this message in
Look here: http://folding.bmc.uu.se/remd/
2013/4/23 bharat gupta bharat.85.m...@gmail.com
Dear gmx users,
I am planning to run REMD for a peptide (406 atoms )+ solvent system
(27639). The temperature range I selected is from 300 to 500. I want to
select appropriate temp. for 56 replicas.
Dear Gromacs users,
In forcefield of my system, I have non-bonded function of the form U
= A*exp(-Brij) - C/(rij^6) - D/(rij^4), for this I wanted to use tabulated
potentials. I have defined functions f(r), g(r) and h(r) as the following,
f = 1/r;
fprime = 1/(pow(r,2));
g =
Dear Gmx users,
My protien has got some strong acidic and strong basic parts. I fold and
unfold my protein with different temperaturss. I bserved high affinity of
those regions towards each other, they are very close to each other over
the simulation.
How can I possibly check whether my two
Thanks. Which tool would provide me vectors over a time?
Steven
On Thu, Apr 18, 2013 at 8:17 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Chapter 8 is your friend. Find a tool to feed data to g_analyze.
Mark
On Wed, Apr 17, 2013 at 4:23 PM, Steven Neumann s.neuman...@gmail.com
wrote:
I have got the temperature distribution from the same link, but how to
select evenly spaced temperatures for 56 replicas, I need to know that
On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal deviceran...@gmail.comwrote:
Look here: http://folding.bmc.uu.se/remd/
2013/4/23 bharat gupta
I don't understand your question. If you got the temperature distribution,
what else do you need?
2013/4/23 bharat gupta bharat.85.m...@gmail.com
I have got the temperature distribution from the same link, but how to
select evenly spaced temperatures for 56 replicas, I need to know that
On
Sorry for that, I explain it again. Actually, I used the this link to
generate a temp. distribution. But I can do REMD for 56 replicas only, as I
have 56 processors available. The t-remd calculator provides 220
temperature values :
300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14,
Thanks, now it's clearer.
Now, how can I temp. from these, so that the replicas can exchange ...
You can't, I would say. The system you have requires so many replicas to
exchange properly from the two temperature extremes you set up. As you have
seen, if you pick up temperatures in that range
Hi,
The PME settings you mention won't make any difference.
I don't see anything that can explain the differnce.
But are you sure that the difference is statistically relevant?
How did you determine sigma?
There could be long time correlations in your system.
Have you check the temperature? You
But if I choose a smaller temperature range , would it be possible to
observe any folding event ??
On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal deviceran...@gmail.comwrote:
Thanks, now it's clearer.
Now, how can I temp. from these, so that the replicas can exchange ...
You can't, I
On 4/23/13 6:37 AM, Steven Neumann wrote:
Dear Gmx users,
My protien has got some strong acidic and strong basic parts. I fold and
unfold my protein with different temperaturss. I bserved high affinity of
those regions towards each other, they are very close to each other over
the
On 4/23/13 1:31 AM, jhon michael espinosa duran wrote:
Hi guys
I have a problem with the MD simulation of C2160 (Fullerene)
with doxorubicin molecules inside. I have a OPLS force field
for C60 that I am using for C2160, and for Doxorubicin, I generate
the force field using PRODRG.
The problem
Thank you.
Steven
On Tue, Apr 23, 2013 at 1:23 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/23/13 6:37 AM, Steven Neumann wrote:
Dear Gmx users,
My protien has got some strong acidic and strong basic parts. I fold and
unfold my protein with different temperaturss. I bserved high
Dear Berk, dear mailing list,
On Apr 23, 2013, at 2:18 PM, Berk Hess g...@hotmail.com wrote:
The PME settings you mention won't make any difference.
Thanks for clarification. I was expecting that but they somehow were the best
candidates in my view.
I don't see anything that can explain the
Who knows? It depends on the size of your peptide, on the energy landscape,
on how long is the run you plan to do. I would bet on no, however.
2013/4/23 bharat gupta bharat.85.m...@gmail.com
But if I choose a smaller temperature range , would it be possible to
observe any folding event ??
Shall I specify one index group for two regions or 2 seprate? g_mindist
asks just for one group.
would twice as cutoff would be sufficent to assess they do not interact?
On Tue, Apr 23, 2013 at 1:54 PM, Steven Neumann s.neuman...@gmail.comwrote:
Thank you.
Steven
On Tue, Apr 23, 2013 at
On 4/23/13 9:15 AM, Steven Neumann wrote:
Shall I specify one index group for two regions or 2 seprate? g_mindist
asks just for one group.
If it only takes one, then you can only give it one.
would twice as cutoff would be sufficent to assess they do not interact?
Probably, maybe less,
So, my final question is whether is possible to do REMD for my system,
using the computational resource that I have.
On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal deviceran...@gmail.comwrote:
Who knows? It depends on the size of your peptide, on the energy landscape,
on how long is the run
Dear Users,
Does any one know which command is capable to return the vector of a
specified group of 2 atoms (e.g. C=O in protein) over the simulation time?
Steven
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Thanks a lot
Steven
On Tue, Apr 23, 2013 at 2:18 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/23/13 9:15 AM, Steven Neumann wrote:
Shall I specify one index group for two regions or 2 seprate? g_mindist
asks just for one group.
If it only takes one, then you can only give it one.
Dear Justin,
Sorry for the confusion.
What I was trying to explain is pdb2gmx output of topol.top file shows the
detection of heme (FE) bound with histidine (NE2) atom but missing to mention
the gromacs bond, angle, dihedral type code.
Which clearly means that pdb2gmx to not able detect
It depends on what you want to do. Possible it is certainly possible, but
you can't be guaranteed to observe the conformational changes you desire to
observe. Again, it does not depend only on the REMD, but also on the length
of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also
In general, look in the literature what other people have done on similar
systems, and try to go from there.
2013/4/23 massimo sandal deviceran...@gmail.com
It depends on what you want to do. Possible it is certainly possible, but
you can't be guaranteed to observe the conformational changes
Thanks a lot for your prompt responses. By using implicit solvent , I am
getting on 9 temperature values. I think this should work , I will try it
out. Also, i checked that when the no. of water molecules are reduced , the
no. of temp. values are also reduced. If I reduce the no. of water
In general, the smaller is your system, the less temperatures you will need
(and you'll have better performance).
Notice however that implicit solvent, while surely a possibility worth
considering, is not usually considered to be very good -take care that if
you write a paper from implicit
Justin,
as the example I have 2 systems consisted of receptor completed with 2
different ligands.
After 100ns of production run I've realized that both of that ligands has
the same degree of conformational dynamics on internal degrees of freedom (
the same RMSD as the measure of internal
On 4/23/13 9:27 AM, Steven Neumann wrote:
Dear Users,
Does any one know which command is capable to return the vector of a
specified group of 2 atoms (e.g. C=O in protein) over the simulation time?
Not directly, but you can probably use g_traj and post-process the coordinate
information.
On 4/23/13 9:36 AM, 라지브간디 wrote:
Dear Justin,
Sorry for the confusion.
What I was trying to explain is pdb2gmx output of topol.top file shows the
detection of heme (FE) bound with histidine (NE2) atom but missing to mention the
gromacs bond, angle, dihedral type code.
Which clearly
On 4/23/13 10:18 AM, James Starlight wrote:
Justin,
as the example I have 2 systems consisted of receptor completed with 2
different ligands.
After 100ns of production run I've realized that both of that ligands has
the same degree of conformational dynamics on internal degrees of freedom (
Dear GMX user,
Are you aware of a GROMACS topology implementation of the recent
dihedral corrections to CHARMM22/CMAP given by RB Best et al., JCTC,
2012, 8, 3257-3273?
If this has already been done, would you be kind enough to send me the
updated files?
Best regards,
Guilherme
--
Prof.
Dear Gromacs Users,
I have simulated a protein with different ions and same substrate bound to
it in POPC lipid bilayer using Groamcs 4.5.4. The ion binding and substrate
binding sites are coupled. After Md simulation we see a reorganization of
these sites. Now, we are trying to calculate the
The .xvg file is a text data file, it is not a graph.
That means you can use whatever your favourite graphing software is to plot the
data: xmgrace, gnuplot, MS Excel, Sigma Plot etc.
If you are using Excel, which it appears you are, then you simple import the
data file into your spreadsheet
Dear Justin/Mark,
I have asked this question previously in the forum, I got some reply from
other members. It will be more useful if you can provide you expert
comments on the same. I am planning to run REMD for a peptide (406 atoms )+
solvent system (27639). The temperature range I selected is
Dear,
In my system ,the loop is part of the active pocket of the protein. when
the ligand is absent, the loop is disordered and if the ligand is present , the
loop can transform into helix.
In order to simulate the disordered loop transform into helix , i should
build a model thant the
Hi,
For the first part of your problem, I would suggest to visit this online
server where you can model your loop, http://falc-loop.seoklab.org/ . It
utilizes homology modeling kind of analogy to add the loop.
Time span within which a disordered loop gets converted to alpha-helix is
not so
Hi,
Steps to get a plot in jpeg, png etc. format are
xmgrace plot.xvg -free
go to the print setup option
choose any option as jpeg, png etc. present in a specific box
then click the print option at the left. It'll export the image file in
jpeg or png format. Now you can use these images
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