Thanks for the response. On further investigation, the problem only seems
to occur in jobs running via MPI on our GPU-enabled nodes, even if the
simulation in question doesn't use GPUs. Re-compiling gromacs 4.6.3 without
CUDA support eliminates the memory-hogging behavior. However, I'd like to
actu
Dear Gromacs users
-- Iam trying to perform free energy calculation for
protein-ligand complex.
--Can any one plz suggess an appropriate tutorial to be
follow to perform this analysis
--
Thanks & Regards
N.NagaSundaram
--
gmx-users mailing listgmx-users@gromacs.org
http
Hi
I have been trying to run simulation on a cluster consisting of 24 nodes
Intel(R) Xeon(R) CPU X5670 @ 2.93GHz. Each node has 12 processors and they
are connected via 1Gbit Ethernet and Infiniband interconnect. The batch
system is TORQUE. However due to some issues with the parallel queue I have
Re: [gmx-users] BGQ compilation with verlet kernels: #include
file"kernel_impl.h" not found.
Side note: On a Blue Gene/Q machine this particular version of Gromacs
is 2.5x times faster than the regular one. I really hope thw BGQ
accelerated kernels will go into the main branch soon.
Dear users,
Recently I have been trying to use "xdrfile" libray to read trajectory
".trr" file in my own C++ code. Now I can just read the coordinates of all
atoms at each time frame. But I don't know how to select certain types of
atoms from the trajectory file. Although the graomcs tool "make_n
It is only a simple question, not a criticism of any kind. I'm sure there
may be perfect reasons to choose one implementation over another. To
someone who is not familiar with the history of gmx development, it is
something to be aware of. That's all.
On Wed, Sep 18, 2013 at 4:56 PM, Mark Abraham
Implementation and description of a model physics are two different
things. You could compute KE of a particle with 0.5 * m * v^2, but if
the mass is used nowhere else, why wouldn't you pre-multiply the mass
by 0.5?
Mark
On Wed, Sep 18, 2013 at 4:31 PM, Guanglei Cui
wrote:
> hmm, does that mean
hmm, does that mean the gmx force field file format or specifications are
not backward compatible?
On Wed, Sep 18, 2013 at 4:08 PM, Mark Abraham wrote:
> There are technical differences between versions about how the VDW
> parameters are computed. You should not expect .tpr equivalence
> between
There are technical differences between versions about how the VDW
parameters are computed. You should not expect .tpr equivalence
between minor version changes such as 4.0 and 4.6. You need to compile
a 4.0.x grompp to see if your setup is equivalent, but having done so
you should be able to use t
Thanks. gmxcheck is quite helpful. Here is part of the output. It turns out
the difference is mainly in the force field parameters, which indicates the
top file provided may not be the one used to produce the tpr file. Perhaps
it is best to contact the authors, unless the difference is due to certa
Thanks for the follow up.
The take-home lesson is that building for BlueGene/Q is unlike
building for the usual homogenous x86 cluster. You still need an MPI
and non-MPI build, but the latter should be targeted at the front end
(Linux on PowerPC, usually), unless/until GROMACS tools acquire MPI
fu
Update
https://docs.google.com/file/d/0B6Qm4snFANimcmxYVnBOSkNCd2s/edit?usp=sharing
Seems I had to declare the atoms in .rtp with + and - when they are across
periodic boundary.
The new movie is showing that atoms do move, but not across the box. Yes, I
would have to play a little ore with param
That -om mechanism has been broken for about a decade, unfortunately.
You will need to include the file, or post a link a file, not attach
it, if you want users of this list to see it.
gmxcheck to compare your new and old .tpr files is useful to see what
you might need in the new .mdp file to rep
On restraining bonds:
The atom moves across the basic unit, i.e. it is not recognising that it
should bond via periodic_molecule
Error: The charge group starting at atom 2833 moved than the distance
allowed by the domain decomposition (1.615483) in direction X
In any case (restraining or not all
On 9/18/13 9:57 AM, Valentina wrote:
Bonds are harmonic. I can test it by restraining them? For purpose of testing
I can even make the topology bond to be 2.06, as in the input file.
Constraints would probably fail, given the relatively large change in geometry.
You can try, but I'd suspec
Bonds are harmonic. I can test it by restraining them? For purpose of testing
I can even make the topology bond to be 2.06, as in the input file.
My system shouldn't be any different from a mice sheet, for instance. Both
have Metal - O bonds that continue through the sheet. What do you mean by
"t
Thanks very much, Szilárd.
Our IT just found out we purchased the latest Intel compiler, but
apparently was never installed. Now, I can check if this happens with the
new compiler. I may or may not follow up with a bug report if I can't
reproduce the behavior.
Regards,
On Sun, Sep 15, 2013 at 1
gmxdump -om writes out a mdp file based on the tpr, but that is not read by
grompp. I tried to change or comment out mdp options that are not
recognized by grompp. It is attached here. The simulation soon crashes with
LINCS errors after 25 steps, while the original tpr runs properly. I'm not
sure w
On 9/18/13 9:09 AM, Valentina wrote:
Thank you,
Yes.
The bond between Al and O is 1.96 A
So it should be within 10% from 2.06 A, so the lowest size is 1.854 A? It
should be able to pick up 1.96 A then. Am I right?
In theory, that bond should work. It looks like a pretty complex system thou
Thank you,
Yes.
The bond between Al and O is 1.96 A
So it should be within 10% from 2.06 A, so the lowest size is 1.854 A? It
should be able to pick up 1.96 A then. Am I right?
--
View this message in context:
http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011284.html
Sent from
Look at the numbers, count the number of atoms you expect in each
moleculetype, and work out what the mismatch is.
Mark
On Wed, Sep 18, 2013 at 2:58 PM, naresh_sssihl wrote:
> Dear GMX users,
>
> I am trying to simulate a protein in SDS/Water box.
>
> 1. No problems with pdb2gmx - .gro file and
Dear GMX users,
I am trying to simulate a protein in SDS/Water box.
1. No problems with pdb2gmx - .gro file and .top files were generated.
/pdb2gmx -f protein.pdb -o protein_pro.gro -water spce/
selected ff 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
2. Created a Cubic box usin
On 9/18/13 8:34 AM, Valentina wrote:
Justin Lemkul wrote
On 9/18/13 8:07 AM, Valentina wrote:
Thank you!
Yep, they seem to be wanting to bond to the O's within the cell, while
they
are meant to bond across the PBC.
I am not sure how periodic_molecule = yes part functions. I don't seem to
ge
Hello. I was calculating the viscosity of hexane through the Gromacs
command g_energy. Three files are generated: visco.xvg, evisco.xvg and
eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but
the value does not match the experimental. I used 8 ns simulation at
equilibrium. Ho
Justin Lemkul wrote
> On 9/18/13 8:07 AM, Valentina wrote:
>> Thank you!
>>
>> Yep, they seem to be wanting to bond to the O's within the cell, while
>> they
>> are meant to bond across the PBC.
>>
>> I am not sure how periodic_molecule = yes part functions. I don't seem to
>> get difference if I t
On 9/18/13 8:07 AM, Valentina wrote:
Thank you!
Yep, they seem to be wanting to bond to the O's within the cell, while they
are meant to bond across the PBC.
I am not sure how periodic_molecule = yes part functions. I don't seem to
get difference if I turn it on or off when I do Energy minimi
Thank you!
Yep, they seem to be wanting to bond to the O's within the cell, while they
are meant to bond across the PBC.
I am not sure how periodic_molecule = yes part functions. I don't seem to
get difference if I turn it on or off when I do Energy minimisation. Do you
have some examples that wo
You mean this one?
http://gromacs.5086.x6.nabble.com/The-computational-methods-used-in-Gromacs-td5011269.html
you have posted it in Gromacs general forum, but checking for it in Gromacs
Users forum (i.e sub-forum) hence don't see it!
V
--
View this message in context:
http://gromacs.5086.x6.
On 9/18/13 5:42 AM, Valentina wrote:
Hello!
I have a surface, formed by Mg2Al(OH)6.
All of the O are bonded with Al, by such forming a mesh.
I am using periodic_molecule=yes
as discussed in this thread:
http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-td501019
Hi everybody!
I have a question about free energy computation.
What algorithm i should use for constraining h-bonds SHAKE or LINCS then i'm
doing free energy computation?
Is any sufficient difference is exist?
Sergey.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/SHAKE-or-
Hello!
I have a surface, formed by Mg2Al(OH)6.
All of the O are bonded with Al, by such forming a mesh.
I am using periodic_molecule=yes
as discussed in this thread:
http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-td5010192.html#a5010234
I set up the topology fo
Hi Shahab,
That site has a lot of structures. It would be better to explicitly state
which one you took. However, in this case, the better question is, how did
you write the topology, and did you check the correspondence of the order
of molecules/atoms in the topology file and the structure file?
Dear Tsjerk
Thanks for your consideration.
My system contains 2 components: (DOPC & cholesterol) lipids + water
molecules.
I get force field parameters from lipid book (for dopc and cholesterol).
I used input coordinate file (system.gro) from following web site:
http://people.su.se/~jjm/Stockh
33 matches
Mail list logo
