Dear gmx-users, dear Mark,
the soap-opera is going on... and I am so sorry to bother you again and
again (but I hope that this will be of help for future people that will
have the same problem...).
Summary of the last episode: I found a way to convert the parameters of
dihedrals and impropers cal
Dear Gromacs users,
I would like to do side-chain dihedral angle PCA for my protein. The
protein contains 293 residues. I came across an explanation about dihedral
PCA in gromcas website (
http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA). Is it possible
to do side-chain dihedral PCA usin
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
---
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" wrote:
> On Tue, Apr 9, 2013 at 11:38 AM, Andrew DeYoung >wrote:
>
> > Hi,
> >
> > For the pas
On Apr 10, 2013 3:34 AM, "Benjamin Bobay" 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 was
>
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
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 w
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 de
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
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 wrote:
> Is oscillation is because of change in hydrogen bonded distance?
>
> Do pr
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 D
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 the
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'll check out chapter 5. And look for those scripts that you mention.
Thanks Justin!
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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 -DCUDA
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 introducin
On Tue, Apr 9, 2013 at 12:21 PM, Andrew DeYoung wrote:
> 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 -
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 ter
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 using
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 wrote:
>
>
>> On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal
>> wrote:
>>
>>> Hello,
>>>
>>> I am calculating the hydrogen bond autocorrelation function us
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
-DCUDA_PROPAGATE
> On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal
> wrote:
>
>> 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.
>>
On Tue, Apr 9, 2013 at 11:38 AM, Andrew DeYoung wrote:
> 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
> proces
On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal wrote:
> 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
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
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 atoms
On Tue, Apr 9, 2013 at 9:59 AM, Lara Bunte 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 "building block"
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 dinucleot
On Tue, Apr 9, 2013 at 9:59 AM, James Starlight 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
> systems in the Charm f
On Tue, Apr 9, 2013 at 8:29 AM, Shine A 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 part?
Doing a simulat
On Tue, Apr 9, 2013 at 12:26 PM, Anna Marabotti 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 it to the gmx-u
On Tue, Apr 9, 2013 at 10:44 AM, Nikunj Maheshwari
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 using polynomial fit
On Tue, Apr 9, 2013 at 8:33 AM, Dr. Vitaly Chaban 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 recollect that
On Tue, Apr 9, 2013 at 5:19 AM, gromacs query wrote:
> 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.
On Tue, Apr 9, 2013 at 3:18 AM, aixintiankong 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 CYS2.
>
The above
On Tue, Apr 9, 2013 at 2:13 AM, Ashalatha Sreshty wrote:
> 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 caten
On Tue, Apr 9, 2013 at 8:02 AM, Za Pour 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 not? I mean d
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 simulation?
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 simulation?
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 w
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 kno
> 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
On Tue, Apr 9, 2013 at 11:03 AM, fantasticqhl wrote:
> 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?
http://gromacs.5086.x6.nabble.com/How-to-get-the-number-of-frames-contained-by-an-xtc-trajectory-file-td4998050.html
Cheers,
Tsjerk
On Tue, Apr 9, 2013 at 11:37 AM, Albert wrote:
> Hello:
>
> I am trying to extract last frame of my MD simulations with command:
>
> trjconv_mpi -f s.xtc -s P-i
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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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
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 C2
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
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 have
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 wrote:
> How did you get the final tempe
On Tue, Apr 9, 2013 at 9:39 AM, fantasticqhl 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 some
> QM scannings
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 wrote:
> I've tried one with 666 aa, but with no publishable results.
>
> On 9 Apr 2013, at 09:47, Nikunj Maheshwari
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 bo
I've tried one with 666 aa, but with no publishable results.
On 9 Apr 2013, at 09:47, Nikunj Maheshwari 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 research papers, but could
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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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 d
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 second
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 wrote:
> 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
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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