on aromatics, which can and
should be further refined. All input is greatly appreciated and I'd
especially love to hear from the Gromacs superhero Justin Lemkul. :)
Thanks!
Alex
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You guys have thought of everything, haven't you... :) Thanks.
JL On 3/23/15 9:09 PM, Alex wrote:
Great, thanks.
One other question, just sort of jumping way ahead. Let's say I had a
denaturated protein chain I wanted to drag in a simulation of
translocation. Is there anything in Gromacs
understanding).
There are some reasons I'd like to stick with oplsaa with my project. Not
set in stone, but highly desirable.
Any ideas?
Thanks,
Alex
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syntax to do that?
I just want to define my atoms in a way that supplements (actually,
precedes) what x2top does when the atoms are not specifically labeled.
A tedious solution in my case, but definitely viable, if this works.
Thank you,
Alex
JL On 3/29/15 7:53 PM, Alex wrote:
Another
interactions.
Alex
NKH Hello Gromacs users,
NKH I tried to create a 6.5 nm cubic box of tetrolic acid (otherwise
NKH known as 2-butynoic acid), but the density is too low. According
NKH to this, http://www.chemspider.com/Chemical-Structure.61810.html,
NKH the density should be about 0.964
NKH g/mL
know x2top has limited intelligence, but how is this correct program behavior?
Also, is there any way to tell x2top to copy all bond and angle
parameters from the ff data into the topology the way pdb2gmx does?
Thanks,
Alex
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Building things is not necessary. I just wasn't sure what particular field in
PDB you were talking about. Some indication that it is supposed to
work is enough. ;)
Thanks,
Alex
JL I don't have the time or desire to build something, test it, and give you an
JL absolute answer :) I can only
be extremely useful. One could always use the
default value if no setting is entered.
Could the last point be relayed to the developers? Sounds like a huge
necessity to me, to be honest.
Thank you,
Alex
JL On 3/29/15 4:07 PM, Alex wrote:
Hi all,
I am messing with the OPLS/AA forcefield. The idea
a globally
neutral
system.
Here is the problem: x2top ignores the second statement from above and the
functionalized edge C is assigned #996. Aside from manually modifying
the resulting topology, can we make this distinction stick?
Thanks,
Alex
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Yeah, I know there's that disclaimer. I wonder if this
http://software-lisc.fbk.eu/obgmx/
could be useful. Any comment on this UFF? First time I'm hearing about
it, to be honest. The system I have in mind isn't much beyond CNTs and
nucleotide chains. Well, and water.
Thanks.
Alex
JL g_x2top
just discovered that a bunch of
different atoms isn't set up correctly.
Thanks,
Alex
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come from
solid-state systems and wish I had experience with Gromacs that's
beyond editconf-genbox-pdb2gmx-grompp.
Come to think of it, you'd set up my system in about an hour. Care to
collaborate? :)))
Alex
JL On 3/26/15 6:10 PM, Alex wrote:
Yeah, I agree with Justin, this is pretty half-baked
oplsaa.
Alex
On Thu, Mar 26, 2015 at 3:56 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/26/15 8:30 AM, Smith, Micholas D. wrote:
There was some work on OPLS-AA/L on nucleic acids back in version 3 of
GROMACS. The group that did the work has a website where they discuss the
nucleic
will
try the earlier suggestion and add the bonded definitions on top of
what was suggested.
Alex
JL For this, the cleanest approach is to create a custom force field, and its
JL contents should be rather simple - bonded and nonbonded parameters for some
C
JL type (for the CNT) and whatever
ve in mind is one of those, as I'm sure many other researchers have. It just happens to involve graphene. ;)
So, it may be worthwhile to gain some level of flexibility to define our own bonded parameters, if covalent bond creation/breake is not on the table.
Thanks,
Alex
I was in your
, and the sheet
behaves beautifully and respects my PBC (the box has precise in-plane
dimensions).
I have solvated my sheet with quite a bit of SPC water (~32K molecules), about
to test some
energy minimization followed by a dynamic simulation.
Does the above sound reasonable?
Thanks,
Alex
p.s
Great, thanks.
One other question, just sort of jumping way ahead. Let's say I had a
denaturated protein chain I wanted to drag in a simulation of
translocation. Is there anything in Gromacs for that, aside from fake
charges and external electric fields, or messing with the code itself?
JL Yep.
,
Alex
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of the box with an established potential implemented in Gromacs? Anything that will not involve manual modification of PDBs or writing text-processing scripts will make me very happy.
I will really appreciate any suggestions.
Thank you,
Alex
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Mauricio,
That is very useful, thanks a lot. I'll try it in a bit.
Alex
MEN Alex,
MEN You can use X3DNA to produce any nucleic acid geometry you’d like and
MEN gromacs pdb2gmx will understand it.
MEN For example, to create a single-strand of 16 DNA bases you only need a file
MEN
shouldn't hinder research.
I do think that having a person such as yourself of Justin on my team to implement what I have in mind would speed things up tremendously, but noone seems to be interested, hint-hint. ;)
Thanks,
Alex
Hi Alex,
Writing a sed oneliner is not the same as writing
Great, glad it's working.
I think there was a wrong bond length somewhere in Andrea's tutorial, not sure where exactly (I could be wrong). Look at everything carefully and make sure the bond lengths are at 0.142 nm, because this is what the generator is doing.
Have fun!
Alex
Thank
'constraints = none' in your mdp. Constraint
algorithms generally beloved by the biophysical community will turn
your nanotubes into solid bricks.
Good luck!
Alex
PB Hi everyone,
PB I am new in the Gromacs users community and in the MD field too. However I
PB red a lot and I want to realize simulation
-- and that is all you
need to run a simulation.
Alex
On Mon, Apr 13, 2015 at 5:49 PM, Pierre Bertin bertin...@gmail.com wrote:
Hi Alex,
All right, I red all this weekend and I know how to modify a force field
to add residues (I hope... ahah). I modified OPLSAA force field because I
want
that is broadly inappropriate for solid-state systems. So,
understanding the concept of topology in GMX-like packages is extremely
useful. Gromacs has a manual of outstanding quality, and it should become
your Holy Bible. :)
Alex
On Mon, Apr 13, 2015 at 6:31 PM, Alex nedoma...@gmail.com wrote:
Hi
to be really hardcore about it, and still assume there _is_
such a thing as harmonic restraints, then the timestep of the real world
is your Planck's time. :)
Alex
On Tue, Apr 21, 2015 at 1:36 PM, Marcelo Depólo marcelodep...@gmail.com
wrote:
Thanks Alex. But then, theoretically
of the Nyquist theorem. I believe GMX tests
for high vibrational frequencies according to 20*pi*tau on the left (ten
times the period).
Hope this helps.
Alex
On Tue, Apr 21, 2015 at 1:02 PM, Marcelo Depólo marcelodep...@gmail.com
wrote:
Hi guys!
Is there a maximum value of Force Constant
Correction: tau/pi on the left for the highest value and 5*tau/pi for the
10 x period suggestion above.
On Tue, Apr 21, 2015 at 1:13 PM, Alex nedoma...@gmail.com wrote:
I think this can be estimated from a general physical argument. The
absolute max in my opinion should come from
4*pi*tau
, but this is the paradigm.
Good luck!
Alex
MC I run a graphene nanolayer, usin the below description (from previous mail.
MC Now i got an other error. It look like there is a conflict in a force
MC field system, someone can suggest me how to modify it?
MC the force field file came from Minoia
, nothing chanes.
Alex
B Dear All,
B
B By H++ and reduce we can have the input PDB for pdb2gmx have the
B initial corrected protonated states for some residues, for example,
B HIS, ARG, GLU and terminal residues. However biologically speaking with the
change of the protein
B conformation
that. :)
Thanks,
Alex
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Well, none of us in this project have the scripting skills necessary for this, that's sort of the problem...
Thanks,
Alex
Hi Alex,
I think the best way is to extend the chain, such that you get an overlap between both ends. So for a stretch of DNA
ACGT
You would generate
TACGTA
. Is it that the utility behavior
cannot be changed at the ff level, and thus our only
option is manual modification of the topology?
Thank you,
Alex
JL pdb2gmx isn't designed to intuitively handle such cases. The best way to go
JL about it is:
JL 1. Run pdb2gmx normally to add H that you might
the particle.
Actually, come to think of it, my Planck time estimate for Mother
Nature's timestep in vibrating bonds is probably incorrect. Effective bond
length over the speed
of light is more like it. :)
Alex
DvdS But it boils down to that if you make the force constant very large you
DvdS need
correspond to what he's got.
Alex
MC Hi,
MC i am trying to model a Graphene nano sheet GNS on Gromacs-
MC I follow the advices about the nanotubes presented in the help site.
MC _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_
MC I run this command to greate the topology:
MC
pbc, but we're not using it here. So, no topology in sight.
Any ideas?
Thanks,
Alex
p.s. I can post the test structure if there's any doubt about periodicity
of the structure itself.
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to actually read the manual on the definition of
angles and dihedrals.
Energy minimization destroys the sheet, because there's a mess in your
setup.
Alex
MC Hi people,
MC I was able to run the graphene layer sheet, by follow your advices.
MC I had a problem with the dihetral angle,
MC i solved
Yeah, I was trying to avoid that last part. You can tell by now how much I
dislike uhm doing work. :) I'll try it, thanks.
Alex
JL 4. Manually edit the topology to introduce the needed bond, angles, and
dihedrals.
JL -Justin
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Well, no, i don't want two. I want one! :)
On Wed, Apr 22, 2015 at 5:17 PM, Ming Tang m21.t...@qut.edu.au wrote:
Hi,Alex
You can try constraint. In umbrella, both 2 groups move.
Sent from my Huawei Mobile
Alex nedoma...@gmail.com wrote:
Hi all,
I have a group (DNA) I'd like
applied to the pulled group. So, if the
periodic option is used, will it be possible to continuously translocate a
linear chain with a length comparable to the corresponding box dimension,
while the rest of the system is non-translating?
Thanks as always.
Alex
On Wed, Apr 22, 2015 at 6:41 PM
That is not an option for me, all groups must exhibit full dynamics, so
partial restraint seems like a decent option.
It is my understanding that explicitly moving only one group is impossible
in the new version. Is that the case?
Thanks,
Alex
On Wed, Apr 22, 2015 at 5:58 PM, Ming Tang m21.t
0.000 0.000
2GRA C2 -0.123 0.071 0.000
3GRA C3 -0.123 0.213 0.000
4GRA C4 0.000 0.284 0.000
5GRA C5 0.246 0.000 0.000
thanks
Il 22/04/2015 19:46, Alex ha scritto:
Hello,
The forcefields for CNT and graphene
The CNT group is actually very strongly restrained, not the entire atomic
population, but the edges. So, from inspecting my code, everything looks
right?
Thanks,
Alex
Not really. The constraint option keeps a rigid constraint between the
two groups. The umbrella keyword specifies
a single
value. The simulated time is now about 1.5 ns.
Thank you,
Alex
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You don't need to run x2top on the GRO file, you can apply it directly to
the PDB. It seems like the PDB to GRO conversion destroyed the coordinates
due to poor formatting of the initial coordinates. This has nothing to do
with the forcefields or graphene, you may just have a crappy PDB.
Alex
interaction and then
try to use it to parameterize a lower level method such as MD.
Hope this helps.
Alex
MT Dear all,
MT I got a problem when modelling the interaction of a peptide and
MT copper. I am using the force field of opls-aa. The charge of
MT copper atoms are defined as zero and the non
Also, I assumed by copper you meant an actual surface of copper, not
a few copper ions floating in water. :)
Alex
MT Dear all,
MT I got a problem when modelling the interaction of a peptide and
MT copper. I am using the force field of opls-aa. The charge of
MT copper atoms are defined as zero
,
which once again could include the time step.
Diamond structure, if properly set up, should be quite rigid, even if
your bond/angle terms are somewhat off, because, well, it's the
diamond structure.
Alex
hy Hi all,
hy My research focuses on the dynamics of a nanodiamond(ND) in a biological
hy
Also, I just looked at your topology. Where are your angles? Try to
implement them and then turn off constraints.
Alex
A Is there a particular reason you're applying LINCS constraints to your
A diamond structure? Usually, LINCS gives convergence
A errors/warnings if the system is poorly
appreciate it if you let me know. :)
Alex
On Thu, Apr 30, 2015 at 2:04 PM, Jarrett Lee Wise jwi...@uwyo.edu wrote:
Hello all-
I am trying to run simulations containing supercritical CO2 and oil
asphaltenes. I have tested various force fields (TraPPE flex, TraPPe
rigid, Charmm, EPM2, Cygan
sha nedoma...@gmail.com wrote:
You said you found the rtp entry to be correct, and yet the one you attached has no angles listed, none whatsoever.
Alex
Thank you for your reply.
I am simulating a PLGA (poly lactic co-glycolic acid molecle).
I get the topology file and I solvated the molecule.
grompp complaining about in your case.
Alex
Dear Sir
I am using oplsaa force field.
In the .rtp file i did not found angles secion for any amino acid.
yes there are sections for dihedrals and impropers.
sorry for troubling you.
Best
Anurag Dobhal
Juniour Research fellow
Supervisor: Dr
, or stick them into your ffbonded. Am I missing something here?
Alex
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. :-)
Alex
On May 4, 2015 11:31 AM, Justin Lemkul jalem...@vt.edu wrote:
On 5/4/15 1:06 PM, Alex wrote:
JL 2. As far as bonded interactions are concerned, in the .rtp only
[bonds] are
JL required to define connectivity. Remaining bonded interactions are
then deduced
JL from bond
With opls-aa, incorrect densities and diffusivities were calculated
entirely away from the critical point for several liquids.
Alex
On May 1, 2015 11:40 AM, V.V.Chaban vvcha...@gmail.com wrote:
This problem is natural. Even small change in (T,P) in the
supercritical range results in a huge
Only other suggestion I have is that 5 ns production runs are probably not
long enough. Granted, we needed diffusion data, so I believe I had 50 to
100 ns long simulations, but even for the barostat to settle, it may be a
good idea to have simulations significantly longer than 5 ns.
Alex
On Thu
bond polarity is significantly
different in the supercritical state and in the gas state.
On Fri, May 1, 2015 at 3:30 PM, Alex nedoma...@gmail.com wrote:
I wasn't talking about the initial post. I was talking about the fact
that in _very stable_ states the same numerical simulation
I wasn't talking about the initial post. I was talking about the fact
that in _very stable_ states the same numerical simulation with a
supposedly well-established set of interactions produces garbage.
VVC The point is that any metastable state in numerical simulations
VVC requires fine-tuned
A cursory search yields:
http://www.sciencedirect.com/science/article/pii/0009261496003971#
http://www.sciencedirect.com/science/article/pii/S0009261403006407
http://link.springer.com/article/10.1007%2Fs11814-011-0248-5
The first one has some parameters, maybe trying them would be a start.
Alex
That's a pretty poorly formed question, including the part where you
actually calculate the epsilon-rf value. Can you please try again with
a description of your system?
Alex
MK Dear all,
MK I use reaction-field-zero as the coulombtype for my system. I wonder how I
MK should choose the right
electrostatics in general. Given the above, I am not sure I understand what's there to calculate, unless you mean running a simulation and _obtaining_ a dielectric property as a result. In that case, given you system, it is a completely different discussion.
Alex
MK Not a poorly formed but a general
Also, reaction-field-zero, as described here
http://manual.gromacs.org/online/mdp_opt.html
which _only_ works with epsilon-rf=0. Any particular reason for doing
this to your electrostatics?
Alex
MK Dear all,
MK I use reaction-field-zero as the coulombtype for my system. I wonder how I
MK
Yup, that should be physically sound.
Alex
Dear Alex,
I have another question related to coulombtype selection. I dont want to use pbc in my system so, PME and Ewald are not good choices. If I use Reaction-field-zero and define a rcoulomb equal to my system size ( since epsilon-rf is 0
instructions on where to quickly see what you're talking about would be
nice. Once again, this isn't something Gromacs-specific.
Alex
On May 15, 2015 9:17 AM, Golnaz Roudsari golnaz.c...@gmail.com wrote:
Dear gmx-user
I want to simulate graphene and surfactants in water. In most of the paper
they put
Golnaz,
I think you're creating a bit of a mess by replying to the digest. If
you don't mind, please see my answer directly to your specific
question, where I will also quote your message from below.
Alex
GR Thank you Alex
GR First of all it is better to say that I am a beginner. I follow two
, although I only use it as a viewer.
There's little to add at this point: learn the tool(s) of your choice and use them to manipulate your coordinates.
Alex
GR Thank you Alex
GR First of all it is better to say that I am a beginner. I follow two papers
GR for my project. The authers are ''Tumala
anything.
Alex
On Thu, May 14, 2015 at 10:35 PM, saeed poorasad s_poora...@yahoo.com
wrote:
Dear Gromacs users ,
Greetings .I am looking for XYZ or PDB file of Carbon nanotube '
Y-junction' .
I will be grateful if you can let me know how i can find or make it .
Thanks in advance .Best
For fullerenes, follow http://www.webcitation.org/66u2xJJ3O and use x2top
to build the topology based on OPLSAA.
Alex
On Wed, Apr 15, 2015 at 12:51 AM, saeed poorasad s_poora...@yahoo.com
wrote:
Hi Gromacs users ,
I want to have a system with one C60 and about 1000 water molecules .I
tried
oscillatory) does not help
with long ref_t
either, maybe try v-rescale.
Alex
n Dear all,
nI am new to lipid simulation. I have downloaded the pope.pdb,
n pope.itp, lipid.itp from Tieleman's web site
n (http://wcm.ucalgary.ca/tieleman/downloads). And I have made a
n directory named
You probably mean the topology, which you will have to build yourself,
likely at the forcefield level. Is there any particular reason for
trying to simulate metal oxide with GMX? There are much better tools
suited for this, e.g. LAMMPS with ReaxFF.
Alex
z Dear you,
z Does
seen by the system (I tracked the errors to the atomtypes).
The dihedral type (3) is listed correctly in the topology. A David Lynch
mystery.
Any ideas?
Thanks,
Alex
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Absolutely nothing in between, this is (cos(45)-cos(phi))^2, two minima at
45 and 315 and a peak around 180. Checked if I converted to R-B
coefficients correctly -- same thing. At 90/270 clean decrease to 45/315.
Alex
On Tue, Apr 14, 2015 at 3:16 PM, Justin Lemkul jalem...@vt.edu wrote
Mark, we just figured it out, thanks. :) And yes, you are definitely onto
something: two identical dihedrals pulling in opposite directions. This is
what happens when people from solid state show up to use GMX. :)
Alex
On Tue, Apr 14, 2015 at 5:20 PM, Mark Abraham mark.j.abra...@gmail.com
wrote
can reveal on a public forum. I hope you'll understand. ;)
Alex
On Fri, Apr 3, 2015 at 1:33 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Alex,
I've done it before, but I can't do it from the top of my head without
seeing the input and checking what Gromacs wants. It's not hard work, it's
Of course, it's not CP2K, which will murder your laptop. :)
Not for long production simulations, but great for
prototyping and shorter tests. Gromacs under Linux is a treat.
Alex
BP Dear users,
BP I perfectly understand that gromacs is not for laptops. However, I was
BP wondering about gromacs
is actually opls_335. Gromacs v.
4.6-beta3. Any ideas?
Thank you,
Alex
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Ah, now I see, thanks. Yes, this entirely follows the paradigm of
biomolecules.
I still insist that Gromacs was a better choice for my project than LAMMPS.
:)
On Thu, Apr 2, 2015 at 12:31 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/2/15 2:28 PM, Alex wrote:
Verlet option did remove
Verlet option did remove that error, thank you. Indeed, there is a large
number of atoms with identical cgnr, no idea why. Does it have to do with
the order of atoms in your PDB?
On Thu, Apr 2, 2015 at 10:22 AM, Justin Lemkul jalem...@vt.edu wrote:
On 4/1/15 7:42 PM, Alex wrote:
I have
...
Thanks for clarifying this, Justin. Kind of a crucial point.
Alex
On Wed, Apr 1, 2015 at 2:26 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/1/15 4:24 PM, Alex wrote:
That is the issue. I AM using -noparam, and x2top is reverting to an
incorrect
bond type. Which then sets off errors in grompp
angle function types (within
GMX convention). I recall posting a while back about properly
parameterizing graphene, and heard mostly meh from the locals (I don't
think you participated in that discussion).
Alex
On Wed, Apr 1, 2015 at 2:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/1/15 4:37
True, true. :)
On Wed, Apr 1, 2015 at 2:29 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/1/15 4:27 PM, Alex wrote:
I think I solved it already, thanks. Entirely due to horrible mess created
by the necessity to create custom atom types. I wish you guys could make
the bond length tolerance
PM, Alex wrote:
I am working with a local copy of oplsaa.ff where I have defined a set of
custom atom types in atomname2type.n2t and added the bond and angle
parameters into ffbonded. x2top creates the topology without issues, but
grompp reports a fatal error (see subject).
The particular type
Mark,
Not to troll, but why did you assume that I didn't do my due diligence before posting here?
Because, you see, you could have left that second part of your reply (which only confirms the legitimacy of my initial question), and it would make it less insulting.
Alex
Hi,
Googling
-repo-ubuntu1404-7-0-local_7.0-28_amd64.deb, followed by the usual
apt-get update/upgrade.
Nvcc reports version 7.0.27.
GMX version is 5.0.5, locally built, with auto-detected options, including
GMX_GPU ON, and GMX_SIMD SSE4.1
On Mon, Jun 8, 2015 at 2:07 PM, Alex nedoma...@gmail.com wrote:
Hi all
is:
mdrun -ntomp 4 file directives
I saw some previous messages on this error, but not sure there's a solution.
Any thoughts? I will provide any additional info as needed. If there are
additional options necessary to debug etc, could you provide the exact
command line?
Thanks,
Alex
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,
Alex
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Thanks for the info. I tried with GMX_EMULATE_GPU=1 preceding the mdrun
line, crashed after 100 steps. Is that the expected behavior?
On Fri, Jun 5, 2015 at 2:46 PM, Szilárd Páll pall.szil...@gmail.com wrote:
On Fri, Jun 5, 2015 at 10:39 PM, Alex nedoma...@gmail.com wrote:
In that case, I am
to include those
flags, but no recompiling is required. Is that correct?
Thanks,
Alex
On Fri, Jun 5, 2015 at 1:52 PM, Szilárd Páll pall.szil...@gmail.com wrote:
Hi Alex,
That's a quite old CPU so it's hard to tell how fast is it, you'll
have to try. There are ways to guesstimate how fast does
the system, but for the heck of
it...
I am now looking at the stats and see that (NxN QSTab + LJ) and (NxN QSTab
[F]) take up about 86% of all flops in my simulation. Which of those get
offloaded?
Thank you,
Alex
On Fri, Jun 5, 2015 at 2:26 PM, Szilárd Páll pall.szil...@gmail.com wrote:
Hi Alex
? A very necessary field of research, IMO.
Alex
MA Hi,
MA You'd have to contact the authors to get their modified version.
MA Mark
MA On Sun, Jun 7, 2015 at 11:09 PM Mostafa Javaheri
javaheri.grom...@gmail.com
MA wrote:
Hi all,
Thanks for your replies,
I searched about the simulation under
. Steered MD is to be carefully designed.
3. Make sure your boundaries are taken care of properly, in case your
pulled object meets the wall.
Alex
hy Hello all,
hy Recently, I preformed a SMD, pulling a nano diamond across the membrane. I
hy found that pull_geometry position in the Gromacs 4.6.5
yesterday about a fatal error due to CPU-GPU sync issue,
but seems like I was able to take care of it.
Very impressed here, about to abandon all of my CPU-only runs and switch to
the GPU node as my workhorse.
Alex
On Tue, Jun 9, 2015 at 3:43 PM, Szilárd Páll pall.szil...@gmail.com wrote
concern is cooling. Comments highly appreciated.
Thanks,
Alex
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of these nanoparticles in vacuum (no
pull code, no solvent, NVE) and look at the kinetic/potential energies
of the system?
Alex
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Peter, it should be in aminoacids, just a legacy file naming.
Alex
On Mon, Jun 22, 2015 at 12:46 PM, Peter Stern peter.st...@weizmann.ac.il
wrote:
Even though it's called aminoacids.n.tdb? Or a different name, e.g.
nucleicacids.n.tdb?
One problem is that I eventually have to deal with tens
post answers that and we'll be getting one, probably
from ASUS. I try to stay away from EVGA (terrible experience, card was
returned, but I kept the Powered by EVGA sticker, which is now
proudly presented on my toilet).
Thanks.
Alex
SP I can't really give you much recommendation in terms
Mark,
I can't really share that particular setup, unfortunately. Let me see if it fails on something I can share.
Alex
Hi,
Having a set of input files that reproduce the problem with x2top uploaded to that redmine will make it more likely that someone will attempt a fix. I'm
, besides having an old version around? I already have
that, and it's a bit less than kosher.
Thanks,
Alex
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with the FDTD method for solving
charge-coupled Maxwell's equations, I am not aware of any tools that can do
this.
Which is kind of strange, because it is both doable and useful.
Alex
MJ Dear Justin,
MJ How could I simulate a membrane protein while there is microwave radiations
in
MJ one
are not even spinning during a single test (mdrun -ntomp 4), and I get massive acceleration. They aren't broken, the card is just cool (small system, ~3K particles).
Thanks,
Alex
Ah, ok, so you can get a 6-pin from the PSU and another from a converted molex connector. That should be just
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