Dear All,
I need help in obtaining frames from every one ps of a trajectory. My
problem is as described:
I obtained a 100ns trajectory, I get one frame for every 5 ps from my
initial, but my new trajectory is generated by catenating different frames
that fall in the bins of PCA space of the
Respected sir,
I successfully completed REMD simulation. Now I am
struggling with analysis part. Here how I select the global minimum from
replica? Can you give some suggestions about the analysis part?
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So there is a problem with your trajectory file. Try to understand what
kind of problem it is.
I can recollect that I experienced something like that why translating CPMD
trajectory to GROMACS. Maybe, it does not write time for each frame at the
right place -- just a guess.
Dr. Vitaly Chaban
Hi. Glad to know that your REMD was successful. We are trying to do the
same, but are stuck in between.
Can you tell us, how did you got the temperature spacing?
Thanks
On Tue, Apr 9, 2013 at 11:59 AM, Shine A shin...@iisertvm.ac.in wrote:
Respected sir,
I successfully
Dear,
In my system ,there are many disulfide bonds in my protein.
i want to split these disulfide bonds to CYSH.
I use these command, pdb2gmx -ignh -f 1AKI.pdb -o 110.pdb -p 110.top -water
spce -ss ,but i get the CYS2.
please help me ,thank you very much!
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The gromacs web page links to this server for REMD temperature generation:
http://folding.bmc.uu.se/remd/
On 9 Apr 2013, at 08:34, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:
Hi. Glad to know that your REMD was successful. We are trying to do the
same, but are stuck in between.
Can you
Hi!
I'm also working on REMD in these days.
For temperature spacing you can use this web site:
http://folding.bmc.uu.se/remd/
In order to find the most probable structure, which should be the global
minimum, I think you can work with cluster analysis based on rmsd. Or it
can be also useful a
Dear Dr. Vitaly Chaban,
Thanks very much for your patient and detailed suggestions on this
problem. Actually, I am doing what your suggested now.
I optimized the copper-ligand complex using QM method, and then did some
QM scannings to derive the bond and angle force constants.
Right now, I am
Dear all...
Does anyone has any idea what is the maximum protein size for which a
successful REMD run has taken place?
We have went through lots of research papers, but could not find any
protein/peptide above 100 aa related to REMD.
We have a protein of 292 aa.
Thanks.
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gmx-users mailing
I've tried one with 666 aa, but with no publishable results.
On 9 Apr 2013, at 09:47, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:
Dear all...
Does anyone has any idea what is the maximum protein size for which a
successful REMD run has taken place?
We have went through lots of
By the way during simulation of the membrane-protein systems in the
Amber99sb ff (with berger lipids) I've noticed decreased of my system in
the Z-direction ( I've observed the same also during simulation of such
systems in the Charm full atomic ff). In both cases the observed effect was
seen in
How did you get the final temperature spacing for the run? Did you get the
fitted values using polynomial fit?
Was the run completed?
On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
I've tried one with 666 aa, but with no publishable results.
On 9 Apr 2013, at 09:47,
On Tue, Apr 9, 2013 at 9:39 AM, fantasticqhl fantastic...@gmail.com wrote:
Dear Dr. Vitaly Chaban,
Thanks very much for your patient and detailed suggestions on this
problem. Actually, I am doing what your suggested now.
I optimized the copper-ligand complex using QM method, and then did
I used the REMD temperature generator. Needless to say, we got really tight
spacing and the enhancement to the sampling was probably small. The whole setup
was pretty experimental. The run was completed.
Erik
On 9 Apr 2013, at 10:01, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:
How did
Thats true with our case as well. The spacing was very small, and we got
almost 70 replicas for our protein between 280-410K.
That's why, we are thinking of any alternate way of getting the spacing,
and started using polynomial fit of the average energies we obtained from
our first run. Do you
Dear Dr. Vitaly Chaban,
Thanks very much again. I am sorry for the unclear, charge transfer was
also taken into account for the complex, I did not mentioned in the last
e-mail.
What do you mean by finite T effect in MD? Kinetics?
For the reproduction of binding energy, I guess I know how to
Dear All,
I have a pdb file in which has only heavy atoms (means all atoms except
hydrogen) and a corresponding itp file with all atoms (including
hydrogens). The heavy atoms in pdb file are in sequence order as in itp
file.
e.g.
itp pdb (no Hydrogens)
*
C1 C1
H1
Gromacs users,
My complex heterogenous system has DPPC+ Protein+ligand. I have packed
lipids around protein and ligand using Inflategro method, (APL: 0.79 nm2 got
after 24th iteration) followed by adding solvent and neutralize the system
by adding CL35 NA 39, since my system has -3.999 non zero
Hello:
I am trying to extract last frame of my MD simulations with command:
trjconv_mpi -f s.xtc -s P-in.gro -dump -1 -o p-out.pdb
but it said:
WARNING no output, last frame read at t=751.4
gcq#286: Oh, There Goes Gravity (Eminem)
thank you very much
best
Albert
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Cheers,
Tsjerk
On Tue, Apr 9, 2013 at 11:37 AM, Albert mailmd2...@gmail.com wrote:
Hello:
I am trying to extract last frame of my MD simulations with command:
trjconv_mpi
On Tue, Apr 9, 2013 at 11:03 AM, fantasticqhl fantastic...@gmail.comwrote:
Dear Dr. Vitaly Chaban,
Thanks very much again. I am sorry for the unclear, charge transfer was
also taken into account for the complex, I did not mentioned in the last
e-mail.
What do you mean by finite T effect
My complex heterogenous system has DPPC+ Protein+ligand. I have packed
lipids around protein and ligand using Inflategro method, (APL: 0.79 nm2
got
after 24th iteration) followed by adding solvent and neutralize the system
by adding CL35 NA 39, since my system has -3.999 non zero total
Dear gmx-users, dear Mark,
I still have problems with my parametrization, and I wrote a message
describing in details the problems, but it appears to be too large and
it is being held on hold (see below). How can I send it to the gmx-users
list? Can I write to personal emails? Please let me
After NVT, usually the lipid bilayer move away from each other creating
some voids, which occurs due to absence of pressure coupling. But its not a
problem. You can go ahead and carry out NPT and see that bilayer has
settled to normal position.
-Anirban
On Tue, Apr 9, 2013 at 3:04 PM, sdshine
Dear All
I have done the lysozyme tutorial and at the end of the simulation a .gro file
have
been produced. would you please tell me whether this gro file contains the
structure
of our molecules at the end of simulation or not? I mean does it show the
simulation
box at the end of
Dear All
I have done the lysozyme tutorial and at the end of the simulation a .gro file
have
been produced. would you please tell me whether this gro file contains the
structure
of our molecules at the end of simulation or not? I mean does it show the
simulation
box at the end of
On Tue, Apr 9, 2013 at 8:02 AM, Za Pour za.p...@yahoo.com wrote:
Dear All
I have done the lysozyme tutorial and at the end of the simulation a .gro
file have
been produced. would you please tell me whether this gro file contains the
structure
of our molecules at the end of simulation or
On Tue, Apr 9, 2013 at 2:13 AM, Ashalatha Sreshty sreshty...@gmail.comwrote:
Dear All,
I need help in obtaining frames from every one ps of a trajectory. My
problem is as described:
I obtained a 100ns trajectory, I get one frame for every 5 ps from my
initial, but my new trajectory is
On Tue, Apr 9, 2013 at 3:18 AM, aixintiankong aixintiank...@126.com wrote:
Dear,
In my system ,there are many disulfide bonds in my protein.
i want to split these disulfide bonds to CYSH.
I use these command, pdb2gmx -ignh -f 1AKI.pdb -o 110.pdb -p 110.top
-water spce -ss ,but i get the
On Tue, Apr 9, 2013 at 5:19 AM, gromacs query gromacsqu...@gmail.comwrote:
Dear All,
I have a pdb file in which has only heavy atoms (means all atoms except
hydrogen) and a corresponding itp file with all atoms (including
hydrogens). The heavy atoms in pdb file are in sequence order as in
On Tue, Apr 9, 2013 at 8:33 AM, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
So there is a problem with your trajectory file. Try to understand what
kind of problem it is.
e.g. by using gmxcheck and/or gmxdump (on a small version of your
data!) to see what information is present.
Mark
I can
On Tue, Apr 9, 2013 at 10:44 AM, Nikunj Maheshwari
nixcrazyfor...@gmail.com wrote:
Thats true with our case as well. The spacing was very small, and we got
almost 70 replicas for our protein between 280-410K.
That's why, we are thinking of any alternate way of getting the spacing,
and started
On Tue, Apr 9, 2013 at 12:26 PM, Anna Marabotti amarabo...@unisa.it wrote:
Dear gmx-users, dear Mark,
I still have problems with my parametrization, and I wrote a message
describing in details the problems, but it appears to be too large and it is
being held on hold (see below). How can I send
On Tue, Apr 9, 2013 at 8:29 AM, Shine A shin...@iisertvm.ac.in wrote:
Respected sir,
I successfully completed REMD simulation. Now I am
struggling with analysis part. Here how I select the global minimum from
replica? Can you give some suggestions about the analysis
On Tue, Apr 9, 2013 at 9:59 AM, James Starlight jmsstarli...@gmail.com wrote:
By the way during simulation of the membrane-protein systems in the
Amber99sb ff (with berger lipids) I've noticed decreased of my system in
the Z-direction ( I've observed the same also during simulation of such
Hello
I read about Gromacs building blocks (
http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks ) and
there is written following table. How to do a MD Smiluation with this building
blocks?
Greetings
Abbrev. Source 2 Full Name
FAD ffgmx.rtp O flavin adenine
On Tue, Apr 9, 2013 at 9:59 AM, Lara Bunte lara.bu...@yahoo.de wrote:
Hello
I read about Gromacs building blocks (
http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks)
and there is written following table. How to do a MD Smiluation with this
building blocks?
A
Hi,
For the past 2 years I have been running Gromacs on a standard Linux cluster
(with nodes containing 24 CPUs). As you know, Gromacs scales excellently
(and is super efficient), and since the CPUs are Intel Xeon 2.4 GHz
processors, the simulations run quite fast (I can run 10 ns of ~7000
Hello,
I am calculating the hydrogen bond autocorrelation function using g_hbond
for O-H---O hydrogen bond in system.
I made two groups 1. O-H atoms numbers 2. two oxygen atoms are interacting
with OH bond.
I am using default hydrogen bond criteria (donor-acceptor distance 3.5 and
angle 30) for
On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote:
Hello,
I am calculating the hydrogen bond autocorrelation function using g_hbond
for O-H---O hydrogen bond in system.
I made two groups 1. O-H atoms numbers 2. two oxygen atoms are interacting
with OH bond.
I am
On Tue, Apr 9, 2013 at 11:38 AM, Andrew DeYoung adeyo...@andrew.cmu.eduwrote:
Hi,
For the past 2 years I have been running Gromacs on a standard Linux
cluster
(with nodes containing 24 CPUs). As you know, Gromacs scales excellently
(and is super efficient), and since the CPUs are Intel
On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal
ndhu...@andrew.cmu.eduwrote:
Hello,
I am calculating the hydrogen bond autocorrelation function using
g_hbond
for O-H---O hydrogen bond in system.
I made two groups 1. O-H atoms numbers 2. two oxygen atoms are
interacting
with OH bond.
Dear experts,
I have the following question. I am trying to compile GROMACS 4.6.1 with GPU
acceleration and have the following diagnostics:
# cmake .. -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DCUDA_HOST_COMPILER=/usr/bin/gcc
There's a known oscillation in the ACF that occurs at ~100 fs or so. Is that
what you see?
Erik
On 9 Apr 2013, at 18:02, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal
ndhu...@andrew.cmu.eduwrote:
Hello,
I am calculating the hydrogen bond
Thank you, Justin. This is very helpful to me, especially the link to the
GPU conference, which I think will be very helpful.
I have done a little benchmarking on our ~7000 atom system, and in those
tests the scaling was excellent -- almost linear when comparing 4, 8, 12,
16, 24 CPUs. I am
Hi
I'm a new user of Gromacs and I want to construct a linear chain of
polytetrafluoroethylene using the force field oplsaa.
I created a work directory and I modified the rtp files by introducing 3
new residues corresponding to my starter of chain (TFEa), my internal
residue (TFEi), and my
On Tue, Apr 9, 2013 at 12:21 PM, Andrew DeYoung adeyo...@andrew.cmu.eduwrote:
Thank you, Justin. This is very helpful to me, especially the link to the
GPU conference, which I think will be very helpful.
I have done a little benchmarking on our ~7000 atom system, and in those
tests the
On Tue, Apr 9, 2013 at 12:21 PM, luanadelore...@libero.it
luanadelore...@libero.it wrote:
Hi
I'm a new user of Gromacs and I want to construct a linear chain of
polytetrafluoroethylene using the force field oplsaa.
I created a work directory and I modified the rtp files by introducing 3
On 2013-04-09 18:06, Mikhail Stukan wrote:
Dear experts,
I have the following question. I am trying to compile GROMACS 4.6.1 with GPU
acceleration and have the following diagnostics:
# cmake .. -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
I'll check out chapter 5. And look for those scripts that you mention.
Thanks Justin!
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Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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gmx-users
Please keep the discussion on the gmx-users list.
On Tue, Apr 9, 2013 at 12:55 PM, luanadelore...@libero.it
luanadelore...@libero.it wrote:
Hi Justin,
thansk for the fast reply.
The exact command is this:
pdb2gmx -ff /home/user01/work/oplsaa.ff/ -f PTFE10.pdb -chainsep ter
I have
The exact command is this:pdb2gmx -ff /home/user01/work/oplsaa.ff/ -f
PTFE10.pdb -chainsep ter
I
have created this directory coping the oplssa.ff directory in share
utilities (I'm an user not an administrator of the pc) and I cannot
modify the original files.
I
attach the files .pdb, and
Is oscillation is because of change in hydrogen bonded distance?
Do program consider the change in hydrogen bonded distance during ACF
calculation?
Nilesh
There's a known oscillation in the ACF that occurs at ~100 fs or so. Is
that what you see?
Erik
On 9 Apr 2013, at 18:02, Nilesh Dhumal
No, this oscillation is related to libration.
See, for instance
http://www.princeton.edu/~fhs/rahman/rahman.pdf
esp. Fig. 24 in this paper
Best regards
Paulo Netz
On Tue, Apr 9, 2013 at 2:38 PM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote:
Is oscillation is because of change in hydrogen
Did you correctly account for the different 1-4 scaling factors in the Berger
and Amber lipids (either by obtaining .itp files from the authors of the Berger
lipids-Amber protein article or making the changes yourself)? If not, then you
are doing your simulation incorrectly (see their paper for
Good afternoon -
I recently installed gromacs-4.6 on CentOS6.3 and the installation went
just fine.
I have a Tesla C2075 GPU.
I then downloaded the benchmark directories and ran a bench mark on the
GPU/ dhfr-solv-PME.bench
This is what I got:
Using 1 MPI thread
Using 4 OpenMP threads
1 GPU
Hi Ben,
That performance is not reasonable at all - neither for CPU only run on
your quad-core Sandy Bridge, nor for the CPU+GPU run. For the latter you
should be getting more like 50 ns/day or so.
What's strange about your run is that the CPU-GPU load balancing is picking
a *very* long cut-off
Szilárd -
First, many thanks for the reply.
Second, I am glad that I am not crazy.
Ok so based on your suggestions, I think I know what the problem is/was.
There was a sander process running on 1 of the CPUs. Clearly GROMACS was
trying to use 4 with Using 4 OpenMP thread. I just did not catch
On Apr 10, 2013 3:34 AM, Benjamin Bobay bgbo...@ncsu.edu wrote:
Szilárd -
First, many thanks for the reply.
Second, I am glad that I am not crazy.
Ok so based on your suggestions, I think I know what the problem is/was.
There was a sander process running on 1 of the CPUs. Clearly GROMACS
Indeed. New players will benefit from
http://www.hpcwire.com/hpcwire/2011-12-13/ten_ways_to_fool_the_masses_when_giving_performance_results_on_gpus.html:-)
Mark
On Apr 9, 2013 5:59 PM, Justin Lemkul jalem...@vt.edu wrote:
On Tue, Apr 9, 2013 at 11:38 AM, Andrew DeYoung adeyo...@andrew.cmu.edu
Mark,
first of all I think that something wrong in amber and charm simulations
because of some fluctuations of the box x-y-z dims during simulation
Energy Average Err.Est. RMSD Tot-Drift
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