Hi all,
I apply a deform at the xy direction of the box, the rate is 0.01 nm/ps but
I met this error :
Warning: Triclinic box is too skewed.
Box (3x3):
Box[0]={ 1.06717e+01, 0.0e+00, 0.0e+00}
Box[1]={ 5.34312e+00, 1.06717e+01, 0.0e+00}
Dear Gromacs users,
As I have referred before I am simulating small molecules (nucleosides)
(around 33 atoms) in vacuum in Gromacs. When I do the simulations at the
end I want to select the most stable structure from the trajectory for the
next steps.
What would be the best methodology to use to
What are you trying to calculate MSD for? I doubt that would be sufficient
sampling to calculate the diffusion coefficient of anything except maybe
water. For lipids, you don't start getting accurate readings until you
reach a **lag** time of 10 ns, and you need 100s of ns of data to get a
good
Thanks, Kevin,
I am looking for the MSD vs lag plot. I use the saved frames that specified
in mdp file. Is that the problem? I saved positions every 10 ps for a 6000
ps simulation. should I lower this or is there another way for using more
trajectories?
On Sun, 19 Apr 2020 at 00:10, Kevin Boyd
Hi,
Are you talking about the reported diffusion coefficient or the MSD vs lag
plot? You should be very careful about where you fit. By default, Gromacs
calculates MSDs at much longer lag times than you typically have good data
for. Use the -beginfit and -endfit options to restrict the fit to the
Unless you give you give details how you calculate the MSD it will not be
possible to help.
Are you using unwrapped co-ordinates in your calculations for MSD?
Arun
On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani wrote:
> Hi,
> I am trying to post-processing my results and calculate MSD (mean
Hi,
I am trying to post-processing my results and calculate MSD (mean square
displacement) but my answer is different from the MSD value that GROMACS
calculated. I use trjconv command and use the output .gro file. I tried to
understand the GROMACS code but I am not a good programmer. Is there any
Dear all,
To generate the initial configurations for umbrella sampling, I conducted a
simple pulling simulation by which a single-small molecule (mol_A) is being
dragged along -Z from water into the body of a thin film.
Since the thin film is large I used *"pull-pbc-ref-prev-step-com = yes" and
Dear gmx users,
I would like to ask whether it is possible to install GROMACS on iPad as
well? Obviously I am not trying to run any simulations on it, but to be able
to generate the run files and to transfer them to a cluster. Does it work
the same way you'll have it on any other MacOS? Of
Hi,
No, some kind of breakage, e.g. a filesystem disappeared, or a file
transfer was incomplete or the file was edited with some inappropriate tool.
Mark
On Sat, 18 Apr 2020 at 11:46, Mijiddorj B wrote:
> Dear Justin,
>
> Thank you very much for your reply. I see. However, I have one more
>
Dear Justin,
Thank you very much for your reply. I see. However, I have one more
question. Is it caused by usage of -noappend or other reasons?
Best regards,
Mijiddorj
-
>
> Message: 1
> Date: Fri, 17 Apr 2020 11:51:25 -0400
> From:
Hello everyone,
I want to create a gap between the first and last strand of a beta barrel
so that I can put a new strand in between.
So, I have generated an input file using charmm-gui and using its gromacs
production file (production.mdp) to run the simulation. I want to use a
harmonic wall
12 matches
Mail list logo
