Hi Users
I am performing a simulation for a bonded metal-protein complex system.
Here I am aware of adding the essential parameters in ffbonded .itp. The
force constant value (kb) in the ffbonded.itp file is calculated using
Gaussian. I would like to clarify the method I have adopted to measure kb
Den 2018-09-11 kl. 17:54, skrev Apramita Chand:
Dear Dr.Spoel,
As suggested, I plotted the correlation function in xmgrace and it looks
fine. I used -fitfn option and also -smooth option ( which If >= 0,
smooths the tail of the ACF by fitting it to an exponential function: y =
Aexp(-x/tau)
Su
Think you better actually post the error message to get some assistance :)
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
BTW, I'd recommend caution when using the dated d.dppc benchmark for
drawing performance conclusions both because it may not be too
representative of other workloads (small size, peculiar settings) and
because it uses all-bonds constrained with 2fs time step which is not
recommended these days (unl
On Tue, Sep 11, 2018 at 5:16 PM Wahab Mirco <
mirco.wa...@chemie.tu-freiberg.de> wrote:
> On 07.09.2018 20:41, Olga Selyutina wrote:
> > ...
> > These sets of CPU and GPU are suitable for price (in our region):
> > *GPU*
> > GTX 1070 ~1700MHz, cuda 1920 - $514
> > GTX 1080 ~1700MHz, cuda 2560 - $6
Hi Peter,
Thank you very much for your suggestion. I will try using atom restraints
and check if the pressure coupling works properly.
Thanks and regards,
Arnab.
On Sep 11, 2018 10:33 AM, "Peter Kroon" wrote:
> Hey Arnab,
>
>
> Why do you freeze atoms instead of putting position restraints? Wh
On 11.09.2018 22:37, Olga Selyutina wrote:
>> How would the 8600K perform without GPU (using the "-nb cpu"
>> option on the mdrun binary)?
> 8600K with frequency 4600Mhz was used
> Command line:
> gmx mdrun -nb cpu
>
> Core t (s) Wall t (s)(%)
>Time: 1529.942 254.99
Hi, Mirco.
2018-09-11 3:29 GMT+07:00 Wahab Mirco :
>
> How would the 8600K perform without GPU (using the "-nb cpu"
> option on the mdrun binary)?
>
>
8600K with frequency 4600Mhz was used
Command line:
gmx mdrun -nb cpu
Core t (s) Wall t (s)(%)
Time: 1529.942 254.99
Hi, Páll
2018-09-11 21:50 GMT+07:00 Szilárd Páll :
> I've presonally not tried the 2nd-gen Ryzen, but based on the performance
> of the 1800X and the compute benchmarks I've seen published, these will
> likely be the best value for money (possibly the 2600X if that allows
> getting better GPUs?)
On 11.09.2018 18:59, Wahab Mirco wrote:
> On 11.09.2018 17:15, Carlos Navarro wrote:
>> I remember that a few years ago, a software was available (link ->
>> http://frolov-pchem.wikispaces.com/Downloads ) that was able to convert
>> .cms parameters (from maestro/desmond to gromacs), but know the li
On 11.09.2018 17:15, Carlos Navarro wrote:
> I remember that a few years ago, a software was available (link ->
> http://frolov-pchem.wikispaces.com/Downloads ) that was able to convert
> .cms parameters (from maestro/desmond to gromacs), but know the link is not
> available anymore.
But it's stil
On 9/11/18 11:09 AM, Gonzalez Fernandez, Cristina wrote:
Dear Gromacs users,
I am trying to reproduce the simulation of a published article and in it the
authors used Particle Meah Ewald for electrostatic interactions with a relative
tolerance of 10^⁻6. I have checked the manual and I only
Dear Gromacs users,
I am trying to reproduce the simulation of a published article and in it the
authors used Particle Meah Ewald for electrostatic interactions with a relative
tolerance of 10^⁻6. I have checked the manual and I only have found tolerance
parameters for energy minimization, nei
On 07.09.2018 20:41, Olga Selyutina wrote:
> ...
> These sets of CPU and GPU are suitable for price (in our region):
> *GPU*
> GTX 1070 ~1700MHz, cuda 1920 - $514
> GTX 1080 ~1700MHz, cuda 2560 - $615
> GTX 1070Ti ~1700MHz, cuda 2432 - $615
> GTX 1080Ti ~1600MHz, cuda 3584 - $930
>
> *CPU*
> Ryzen
Dear all,
I’m trying to obtain the parameters of nitrate for the oplsaa force field
without luck. Doe someone knows a way to obtain parameters for small
molecules, using the oplsaa paremeters?
I remember that a few years ago, a software was available (link ->
http://frolov-pchem.wikispaces.com/Down
Sadly, I can't recommend packaged versions of GROMACS for anything other
than pre- or post-processing or non-performance critical work; these are
compiled with proper SIMD support which is generally wasteful.
Also, I can't (yet) recommend AMD GPUs as a buying option for
consumer-grade stuff as we
Hi,
On Fri, Sep 7, 2018 at 8:40 PM Olga Selyutina
wrote:
> Hi,
> A lot of thanks for valuable information.
> If it isn’t difficult for you, could you answer how the growth of
> performance under using the second GPU on the single simulation was changed
> in GROMACS 2018 vs older versions (2016,
Dear all,
Trying to install the latest version of Gromacs using Cmake version 3.12.2.
Running the following command gives the following output:
~/src/gromacs-2018.3/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON
CMake Error at gromacs/CMakeLists.txt:130 (tmpi_get_source_l
I did not change anything in mdp. I remove surface waters which are making
bad contact to the protein.
On Tue, Sep 11, 2018, 2:30 PM ISHRAT JAHAN wrote:
> Thank u for your instant reply.
> What changes you have done in mdp file to remove core dump error?
>
> On Tue, Sep 11, 2018, 1:26 PM Bratin
Dear Dr.Spoel,
As suggested, I plotted the correlation function in xmgrace and it looks
fine. I used -fitfn option and also -smooth option ( which If >= 0,
smooths the tail of the ACF by fitting it to an exponential function: y =
Aexp(-x/tau)
Surprisingly, for all these options (or without) the
Thank u for your instant reply.
What changes you have done in mdp file to remove core dump error?
On Tue, Sep 11, 2018, 1:26 PM Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
wrote:
> Ya
>
> On Tue, Sep 11, 2018, 12:45 PM ISHRAT JAHAN wrote:
>
> > Did your problem of core dumped was solved?
> >
Hey Arnab,
Why do you freeze atoms instead of putting position restraints? Why not
let the loose entirely? Freezing creates large artefacts.
Second, 4 ns equilibration is *way* too short.
Lastly, see http://www.gromacs.org/Documentation/Terminology/Pressure
Peter
On 10-09-18 19:01, ARNAB MU
Hi,
Yes this is expected. The number of ranks affects what grids may be chosen,
and thus the number of alternatives the optimizer might try. For such a
short run, the optimization is fairly useless, however.
Mark
On Fri, Aug 31, 2018 at 1:21 PM Mahmood Naderan
wrote:
> Hi
> It seems that chang
Ya
On Tue, Sep 11, 2018, 12:45 PM ISHRAT JAHAN wrote:
> Did your problem of core dumped was solved?
>
> On Tue, Sep 11, 2018, 12:23 PM Bratin Kumar Das <
> 177cy500.bra...@nitk.edu.in>
> wrote:
>
> > No problem...I did for other proteins also...during NVT ensemble it's
> > concentration will be
Dear all,
When I am running gmx grompp comand for adding ions the
following warning I am getting. Can It make any problem in md-simulation
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Did your problem of core dumped was solved?
On Tue, Sep 11, 2018, 12:23 PM Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
wrote:
> No problem...I did for other proteins also...during NVT ensemble it's
> concentration will be fixed.
>
> On Tue, Sep 11, 2018 at 11:22 AM, ISHRAT JAHAN
> wrote:
>
>
> Message: 1
> Date: Mon, 10 Sep 2018 22:16:03 -0600
> From: Alex
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Number of glucose molecules
> Message-ID: <4050d74c-3628-a816-62cb-53160ceaa...@gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
Dear Alex
No I am not.
I
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