Hi
I have another question, I used gmx energy to evaluate LJ and electrostatic
interaction, as before discussion LJ is meaningless physically, is there
another module that can predict , polar and non polar interactions accurately?
is this meaningless that you mentioned according to Gromos
This here is pretty useful, as it turns out (наконец-то нормальную
документацию написали):
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
Developers tell us that we can get very good performance without
utilizing all CPU threads. Anyway, if you built gmx with all the
Hey everyone! Could help me somebody, please. I have PC with 8 cores, 16 logical cores and 1 compatible GPU, but gromacs calculates just with 1GPU, 1MPI thread and 8 OpenMP threads. Would it possible for me to use all of 16 logical cores? i7-7820XNvidia Titan Xpgromacs 2018 CUDA=onUbuntu 16.04 --
Question: in the DD output (md.log) that looks like "DD step xx pme
mesh/force 1.229," what is the ratio? Does it mean the pme calculations
take longer by the shown factor than the nonbonded interactions?
With GTX 960, the ratio is consistently ~0.85, with Tesla K40 it's ~1.25.
My mdrun line
I get it now, Thank you very much for your help.
--
This email was Anti Virus checked by Security Gateway.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read
On 6/13/18 7:28 PM, kordza...@aut.ac.ir wrote:
Hi Dr.Lemkul
Thank you very much for your answer,
it means that, LJ contains attraction and repulsion parts that calculate
correspond distance, distance and epsilon,
in my paper, what can I called what obtained from LJ-SR, is it vdW ?
To echo
Hi Dr.Lemkul
Thank you very much for your answer,
it means that, LJ contains attraction and repulsion parts that calculate
correspond distance, distance and epsilon,
in my paper, what can I called what obtained from LJ-SR, is it vdW ?
Thanks in advance for your time and your help
Regards
Azadeh
On 6/13/18 7:16 PM, kordza...@aut.ac.ir wrote:
Hi Dr.Abraham
Thank you very much for your answer, I couldn't recognize my problem that ,
what does LJ-SR indicate in gmx energy module, vdw, polar-polar,
nonpolar-nonpolar or other interactions?
Thanks in advance for your answer and your help
Hi Dr.Abraham
Thank you very much for your answer, I couldn't recognize my problem that ,
what does LJ-SR indicate in gmx energy module, vdw, polar-polar,
nonpolar-nonpolar or other interactions?
Thanks in advance for your answer and your help
Regards
Azadeh
--
This email was Anti Virus
So, swap, then? Thank you!
On Wed, Jun 13, 2018 at 4:49 PM, paul buscemi wrote:
> flops trumps clock speed…..
>
> > On Jun 13, 2018, at 3:45 PM, Alex wrote:
> >
> > Hi all,
> >
> > I have an old "prototyping" box with a 4-core Xeon and an old GTX 960. We
> > have a Tesla K40 laying around
flops trumps clock speed…..
> On Jun 13, 2018, at 3:45 PM, Alex wrote:
>
> Hi all,
>
> I have an old "prototyping" box with a 4-core Xeon and an old GTX 960. We
> have a Tesla K40 laying around and there's only one PCIE slot available in
> this machine. Would it make sense to swap the cards,
That is indeed strange. Could it be because of the compressibility = 0 in
the first coordinate direction? if your simulations start with a badly
adjusted (minimized) structure in the TPR then it might get stuck there
because the 0 compressibility might not allow any change in the box
dimensions
Hi all,
I have an old "prototyping" box with a 4-core Xeon and an old GTX 960. We
have a Tesla K40 laying around and there's only one PCIE slot available in
this machine. Would it make sense to swap the cards, or is it already
bottlenecked by the CPU? I compared the specs and 960 has a higher
Dear all,
I have mixture of two types of short polymer in aqcuse solution on top of a
slab surface. After NVT equilibration, I run NPT with ref-p = 1
semiisotropically, below is part of my npt.mdp file.
I wonder why the pressure in the system is stable around *3* after 3ns
in spite of of ref-p
On 6/13/18 11:11 AM, nik...@tezu.ernet.in wrote:
On 5/31/18 10:54 AM, nik...@tezu.ernet.in wrote:
Hello,
Can anyone provide me with the correct topolgy file for
Adenosine-5'-Monophosphate(AMP).
AMP is part of the CHARMM36 force field. Generate the topology with
pdb2gmx.
>
> On 5/31/18 10:54 AM, nik...@tezu.ernet.in wrote:
>> Hello,
>>
>> Can anyone provide me with the correct topolgy file for
>> Adenosine-5'-Monophosphate(AMP).
>
> AMP is part of the CHARMM36 force field. Generate the topology with
> pdb2gmx.
>
>
Hi,
No single trajectory constitutes an experiment that should be expected to
be replicable. You might have observed where the sun appeares to be at dawn
today, but they observed where it was on November 7, 2014 and neither of
those observations tells you anything about the range of positions the
Hi,
All force fields have functional forms and parameters for them that have
been arbitrarily and empirically determined in ways that they reproduce
some observables. Except if the designers intended some component to have a
physical interpretation, there is none you should make without clear
Hi all
I've simulated interaction of functionalized carbon nanotubes with drug with
Gromos 54a7 force field, by gmx energy module and defining enegy grps I
obtained LJ-SR , short range Lennad-jones potential between drug and CNT, in my
system there are different interavtions, polar-polar,
Hi,
These refer to the twin-range cutoff scheme, which was removed several
years ago. Please do everybody a favour and don't start new work from such
ancient versions. The code and its documentation have been vastly improved
since then.
Mark
On Wed, Jun 13, 2018 at 10:35 AM 张明敏 wrote:
>
>
Dear gromacs users,
I am Surya a Ph.D. scholar from lab of computational biology, CDFD,
Hyderabad. I have done simulations for 100ns of 20 residue length peptide.
I have done dPCA as mentioned in the gromacs tutorial. I have made a
dangle.ndx file with all dihedral angles atom numbers. I
Dear all;
When I set the simulation parameters, I found that there are many settings
about the cut-off radius in mdp file. After looking at manual in detail, I
still have several questions:
1，In the manual 4.5.5(p18 3.4.2, pair lists generation), there are concepts of
"rshort" and
thank you sir,for your suggestion.yes the error was because of version mismatch.
On 6/12/18, Justin Lemkul wrote:
>
>
> On 6/12/18 9:31 AM, SHAHEE ISLAM wrote:
>> hi,
>> i am following this tutorial
>> http://cgmartini.nl/index.php/tutorials-general-introduction/proteins.
>> afrter converting
I just want to quickly add to this discussion, as it may be useful to
others. The acceleration here really appears to be in the sense of p =
rho*g*h, which is hydrostatic pressure at the bottom of e.g. water slab
of height h under "gravity" described by g.
In other words, knowing the box
Kindly look at my query..
Thank you!
On Mon, Jun 11, 2018 at 5:39 PM, Sundari wrote:
> Dear gromacs users,
>
> I am running a simulation of three alpha helical peptides with a carbon
> nano tube in a simulation box. Actually I am following a paper and want to
> reproduce the results.
>
> In my
In g_rdf command, I want to generate rdf between surface of mainchain atoms
of peptide and center of mass of solvent molecules so as to compute the
distance from the
center of mass of each solvent molecule to the van der Waals
surface of every atom in the peptide main chain.
What should be the
26 matches
Mail list logo
