Hi,
One way to check that is to consult the online documentation...
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html shows
options taking dynamic selections!
Mark
On Wed, 27 Feb 2019 at 15:08 Cardenas, Alfredo E
wrote:
> Hello all,
> I would like to calculate the rdf
Hello all,
I would like to calculate the rdf between a set of oxygen atoms in a lipid
bilayer to water. But I would like to include in this calculation only a subset
of these oxygen atoms that come closer (< 0.3 nm) to Ca ions. I wonder if such
a dynamic selection is possible combined with the
*
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Molecular Data co-located with EuroVis 2019 June 3, 2019, Porto, Portugal
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been extended to
Dear Szilárd,
They most certainly are clear! I originally thought the GPU of the terminal
would be very useful. Your suggestions are of great help.
Thank you so much!
Best wishes,
Lalehan
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Hi,
If it was something fundamentally wrong, you'd see an issue before this.
Martini is just inherently a teensy bit unstable - but this is where the
non-reproducibility of simulations comes in handy; restarting from far
enough away will likely avoid a transiently high energy event.
Kevin
On
Hi
OK! I made https://redmine.gromacs.org/issues/2873
Mark
On Wed, 27 Feb 2019 at 00:36 Sergio Perez wrote:
> Hi,
> Thank you very much for the response. I would like to suggest this
> posibility as a feature for future editions :)
> Sergio
>
> On Tue, Feb 26, 2019 at 11:36 PM Mark Abraham
Dear Szilárd
I wrote before because of the error message when keeping occurring for mdrun
simulation:
Assertion failed:
Condition: stat == cudaSuccess
Asynchronous H2D copy failed
As I mentioned all Versions to install (Gormacs, Cuda, nvcc, gcc) are the
newest once now.
If I run mdrun
Thanks Justin. How should I check if there is a Ter between protein and
glucose ? If I get you right, for my protein and Bglc system I just need the
Bgc in the .pdb to be changed to Bglc. Do I need to seprate Bglc from the
protein and follow the tutorial or can it be regarded as a complex of
It does! Thank you
On Wed, 27 Feb 2019, 13:38 Quyen Vu, wrote:
> hope this help
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
> On Wed, Feb 27, 2019 at 2:17 PM antonia vyrkou wrote:
>
> > hello,
> >
> > is there a way to execute an interactive gromacs command (for
Thank you!
On Wed, 27 Feb 2019, 13:38 Justin Lemkul, wrote:
>
>
> On 2/27/19 8:16 AM, antonia vyrkou wrote:
> > hello,
> >
> > is there a way to execute an interactive gromacs command (for example
> gmx
> > rmsf , choosing a group number from an index file) without typing the
> > number but
hope this help
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
On Wed, Feb 27, 2019 at 2:17 PM antonia vyrkou wrote:
> hello,
>
> is there a way to execute an interactive gromacs command (for example gmx
> rmsf , choosing a group number from an index file) without typing
On 2/27/19 8:16 AM, antonia vyrkou wrote:
hello,
is there a way to execute an interactive gromacs command (for example gmx
rmsf , choosing a group number from an index file) without typing the
number but "reading" it from a file or from a while loop?
Does that make sense?
Have you checked gromacs manual? for example version of 2019.1 on page 299
On Wed, Feb 27, 2019 at 2:12 PM 이영규 wrote:
> Dear gromacs users,
>
> These days, I am working on supercritical fluid of lennard jones fluid. I
> want to make a system of supercritical fluid by using gromacs with reduced
Michael,
We have the issue pinned down and will be fixed soon. Thanks for the
feedback.
--
Szilárd
On Tue, Feb 26, 2019 at 5:46 AM Michael Williams <
michael.r.c.willi...@gmail.com> wrote:
> Hi Szilárd,
>
> I think these two files (from the complex/nbnxn-ljpme-LB test, just as an
> example)
The Quadro K2200 is a low-end several generations old GPU and I strongly
doubt you will see any benefit from using it.
I suggest you try running
mdrun -nb gpu -ntmpi 1 -ntomp 36 -pin on
which will give you the (most likely best) performance you can get when
using both high-end Intel CPUs and the
hello,
is there a way to execute an interactive gromacs command (for example gmx
rmsf , choosing a group number from an index file) without typing the
number but "reading" it from a file or from a while loop?
Does that make sense?
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Dear gromacs users,
These days, I am working on supercritical fluid of lennard jones fluid. I
want to make a system of supercritical fluid by using gromacs with reduced
units. However, I am lost defining those parameters in gromacs. Could
anyone help me to figure out this problem?
Thanks in
Dear Szilárd,
There is indeed one GPU. And please keep in mind I used to exploit the -nt
72 option BEFORE the 2019-dev version. It looks like it employs GPU by
default and I don't know how to efficiently use it, apparently. Here is
the info you asked for:
System size: 130655 atoms
.mdp file:
;
Dear Carsten, thank you for your advice. I'd tried gmx mdrun -deffnm
md_0_30 -ntmpi 4 -ntomp 18 -npme 1 -pme gpu -nb gpu, then tried -ntmpi 8
-ntomp 9, later tried -ntmpi 12 -ntomp 6 (the rest of the command being the
same) and I feel like neither of them make much of a difference. The CPU
Hi,
Thank you very much for the response. I would like to suggest this
posibility as a feature for future editions :)
Sergio
On Tue, Feb 26, 2019 at 11:36 PM Mark Abraham
wrote:
> Hi,
>
> Unfortunately there is no simple way to get the last frame. Even gmx
> trjconv -dump doesn't help unless
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