Gromacs Users,
I am interested in implementing a thole polarization scheme in my
simulations of ionic liquids. However, the gromacs 4.5 manual does
not give much information on this feature beyond a brief mentioning.
An example of the implementation can be found in the mailing list at
http://list
Can someone explain to me what "compute a radial membrane normal" means in
the g_order options. I would like to calculate S with respect to the
surface of a spherical particle instead of one of the axes. Is this what
it does?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromac
Reciprocal space error estimate of 3.3 kJ/mol*nm.
On Wed, Feb 29, 2012 at 3:47 AM, Dommert Florian <
domm...@icp.uni-stuttgart.de> wrote:
> On Mon, 2012-02-27 at 11:05 -0700, Denny Frost wrote:
> > The ionic liquid is bistriflate N-methyl-N-propyl pyrrolidinium and
> > the force fiel
these have not
resolved this issue. How can I calculate the error in the electrostatic
force?
Denny
On Sat, Feb 25, 2012 at 4:43 AM, Dommert Florian <
domm...@icp.uni-stuttgart.de> wrote:
> On Fri, 2012-02-24 at 11:03 -0700, Denny Frost wrote:
> > Thank you both for your replies. I
.5e-5
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp= 300.0
gen_seed= -1
On Fri, Feb 24, 2012 at 12:17 AM, Dommert Florian <
domm...@icp.uni-stuttgart.de> wrote:
> On Thu, 2012-02-23 at 13:35 -0700, Denny Frost wrote:
> > Dear all
Dear all,
I am trying to equilibrate a solvent of pure ionic liquid. The system
keeps exploding (after 2-5 ns) and I am not sure why, though I believe
coulombic interactions are to blame. This is because the Coul-SR term is
negative, but the Coul. recip term is very positive throughout the entire
; On 28/10/2011 4:57 AM, Denny Frost wrote:
>
> Dear All,
> I have been trying to install gromacs 4.5.3 on my imac with no success. I
> followed the "quick and dirty instructions" and downloaded openmpi-1.4.2,
> fftw-3.2.2, and gromacs-4.5.3. Unpacked them and ran ./conf
Dear All,
I have been trying to install gromacs 4.5.3 on my imac with no success. I
followed the "quick and dirty instructions" and downloaded openmpi-1.4.2,
fftw-3.2.2, and gromacs-4.5.3. Unpacked them and ran ./config as explained
in the instructions. The openmpi installation says it was succe
On 2011-03-12 17.28, Denny Frost wrote:
>
>> No, it requires six, acutally, for aniisotropic coupling. I decided to
>> use semi-isotropic coupling with the xy compressibilities set to 4.5e-15
>> (it won't accept 0). This should keep the walls parallel to the z axis
>&
, Mar 12, 2011 at 9:24 AM, David van der Spoel
wrote:
> On 2011-03-12 17.17, Denny Frost wrote:
>
>> Thanks for answering that question about dispersion, that makes sense.
>> Also, The values I currently get with NPT are around 58 mN/m, while the
>> average values I get fo
pling in the z direction, but gromacs 4.5.3 won't let you specify tau_p =
0. Any other way to do pressure coupling in just the z direction?
Denny
On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost wrote:
> Is that using anisotropic pressure coupling?
>
>
> On Sat, Mar 12, 2011 at
Is that using anisotropic pressure coupling?
On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel
wrote:
> On 2011-03-12 16.45, Denny Frost wrote:
>
>> I have run NPT simulations using isotropic and semiisotropic coupling
>> with the same results. I have never done co
, it
will make the system closer to experimental values. I will give this a try
and see what happens. My question still remains - why do NPT and NVT
simulations give such different values for surface tension?
Denny Frost
On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi wrote:
> David,
>
>
I am running MD simulations on Liquid/Liquid interfaces and measuring the
interfacial tension between them. I have found that the readings in NVT
simulations are close to experimental values, but have a lot of variation.
I run NPT simulations on the exact same system and find the results show
very
Is tpbconv with the "pbc" option the best way to make the molecules whole
again?
On Wed, Feb 9, 2011 at 2:06 PM, Justin A. Lemkul wrote:
>
>
> Denny Frost wrote:
>
>> This run is actually a combination of two 5x5x5 nm boxes, one if which was
>> previously
n Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul wrote:
>
>
> Denny Frost wrote:
>
>> I'm using version 4.5.3
>>
>> Here's the output from the log file from DD initiation to the error:
>>
>> Initializing Domain Decomposition on 8 nodes
>> Dynam
2.0
ref_p = 1.0
compressibility = 4.5e-5
; Generate velocites is off at 300 K.
gen_vel = yes
gen_temp= 300.0
gen_seed= 10
On Wed, Feb 9, 2011 at 1:39 PM, Justin A. Lemkul wrote:
>
>
> Denny Frost wrote:
>
>> I am trying
I am trying to start a run using domain decomposition on a 5x5x10 nm box
with about 26,000 atoms in it. I've tried running 8-16 pp nodes, but
gromacs always throws an error saying that there is no domain decomposition
compatible with this box and a minimum cell size of 6.728 nm. I've tried
many v
er).
Here is my g_energy command:
g_energy -f md.edr -s md.tpr -o energy.xvg -b 19000 -e 2
I think I might just write a script file to parse the xvg file from g_energy
to get me the correct values.
On Tue, Feb 1, 2011 at 3:31 PM, Justin A. Lemkul wrote:
>
>
> Denny Frost wrote:
I don't have an RMS section on my log file.
The final xvg file that comes from g_energy is much too long to post here,
but contains exactly what is in the log file. The interactive output from
g_energy is, however, thus:
Pressure = 995.9 bar (error = 0.65 bar)
On Tue, Feb 1, 2011 at
wrote:
> On 21/01/2011 10:12 AM, Denny Frost wrote:
>
> Sorry, I'm referring to a lot of runs here - some fluctuate more than
> others and some have greater average values than others. The average value
> is never greater than the maximum fluctuation in each run, so that is n
Since gromacs allows you to use quite a few different force fields with
different naming schemes, how does it know (from reading the topology file)
which atoms are hydrogens to enforce the hbond constraints?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listin
In the log file, when gromacs specifies "Nodes," does it mean processors?
On Fri, Jan 28, 2011 at 1:44 PM, Justin A. Lemkul wrote:
>
>
> Denny Frost wrote:
>
>> I'm leaning toward the possibility that it is actually only running 8
>> copies of the same jo
at 1:32 PM, Justin A. Lemkul wrote:
>
>
> Denny Frost wrote:
>
>> Here's my grompp command:
>>
>> grompp_d -nice 0 -v -f md.mdp -c ReadyForMD.gro -o md.tpr -p top.top
>>
>> and my mdrun command is this:
>> time mpiexec mdrun_mpi -np
s, but I think it's a separate
issue to take up with my supercomputing facility.
On Fri, Jan 28, 2011 at 1:18 PM, Justin A. Lemkul wrote:
>
>
> Denny Frost wrote:
>
>> all 8 nodes are running at full capacity, though
>>
>>
> What is your mdrun command lin
all 8 nodes are running at full capacity, though
On Fri, Jan 28, 2011 at 1:13 PM, Justin A. Lemkul wrote:
>
>
> Denny Frost wrote:
>
>> Here's what I've got:
>>
>> M E G A - F L O P S A C C O U N T I N G
>>
>> RF=Reaction-Field FE=Free
he speed issues.
On Fri, Jan 28, 2011 at 12:46 PM, Justin A. Lemkul wrote:
>
>
> Denny Frost wrote:
>
>> gromacs 4.5.1
>>
>>
> Ah, what I posted was from 4.0.7. I wonder why that sort of output was
> eliminated in 4.5; it's quite useful. Sorry for leadi
gromacs 4.5.1
On Fri, Jan 28, 2011 at 12:40 PM, Erik Marklund wrote:
> PME is still an Ewald sum.
>
> Erik
>
> Denny Frost skrev 2011-01-28 20.38:
>
> I don't have any domain decomposition information like that in my log file.
> That's worrisome. The only ot
26 PM, Justin A. Lemkul wrote:
>
>
> Denny Frost wrote:
>
>> I just realized that that was a very old mdp file. Here is an mdp file
>> from my most recent run as well as what I think are the domain decomposition
>> statistics.
>>
>> mdp file:
>> tit
decomposition
There are: 12800 Atoms
Max number of connections per atom is 63
Total number of connections is 286400
Max number of graph edges per atom is 6
Total number of graph edges is 24800
On Thu, Jan 27, 2011 at 4:32 PM, Justin A. Lemkul wrote:
>
>
> Denny Frost wrote:
>
>>
Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
>
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> *From:* gmx-users-boun...@gr
I am taking over a project for a graduate student who did MD using Gromacs
3.3.3. I now run similar simulations with Gromacs 4.5.1 and find that they
run only about 1/2 to 1/3 as fast as the previous runs done in Gromacs
3.3.3. The runs have about the same number of atoms and both use opls force
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *Denny Frost
> *Sent:* Friday, 21 January 2011 9:23 AM
> *To:* Discussion list for GR
yes
gen_temp= 300.0
gen_seed= 10
On Thu, Jan 20, 2011 at 3:49 PM, Justin A. Lemkul wrote:
>
>
> Denny Frost wrote:
>
>> from -1000 to 1000, depending on the system. The simulation box is 8x8x8
>> nm (roughly) and contains about 12,000 atoms
from -1000 to 1000, depending on the system. The simulation box is 8x8x8 nm
(roughly) and contains about 12,000 atoms
On Thu, Jan 20, 2011 at 3:09 PM, Justin A. Lemkul wrote:
>
>
> Denny Frost wrote:
>
>> I am running a variety of NPT simulations with polar, non-polar, and
9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *Denny Frost
> *Sent:* Friday, 21 January 2
I am running a variety of NPT simulations with polar, non-polar, and ionic
compounds. Although my results for density agree well with experimental
values, the pressures I get from g_energy are off by 1 to 3 orders of
magnitude. In the log file, the pressure fluctuates around a lot from -400
to 40
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