Hi,
When we used 2 GPU nodes (each has 2 cpus and 2 gpus) to do a mdrun(with
no PME-dedicated node), we noticed that when CPU are doing PME, GPU are
idle, that is they are doing their work sequentially. Is it supposed to
be so? Is it the same reason as GPUs on PME-dedicated nodes won't be
use
On Sat, Aug 23, 2014 at 1:47 PM, Theodore Si wrote:
> Hi,
>
> When we used 2 GPU nodes (each has 2 cpus and 2 gpus) to do a mdrun(with
> no PME-dedicated node), we noticed that when CPU are doing PME, GPU are
> idle,
That could happen if the GPU completes its work too fast, in which case the
en
Dear gromacs users, I am trying to use an electric field which is varying
with time. I read the previous posts and successfully generated time
varying electric field with E-xt, E-yt and E-zt.
but I need an electric field which has an initial phase term (ie. of the
form E= E0cos(2*pi*f*t+some angle
Dear Gromacs experts,
This time I have a question not regarding Gromacs itself but rather MD
analysis in general. Let's say that I want to plot the distance between
water and atom of an amino acid residue forming hydrogen bond. Now, how can
I do it when water is donor of this h-bond and water mole
Hi Dawid,
In my understanding, a hydrogen bond is considered between one set of
hydrogen-donor-acceptor in Gromacs. So, when your water molecule flips and
its oxygen becomes the acceptor, it is considered as a different hydrogen
bond. So, the plot you have two hydrogen bonds each with differing
li
Hi,
Section 4.2 of the manual has a discussion of dihedrals. The section
contains, in part, the following text:
"With the periodic GROMOS potential a special 1-4 LJ-interaction
must be included; with the Ryckaert-Bellemans potential _for alkanes_ the
1-4 interactions must be excluded from the n
Hi gromacs users,
I met a problem with too much PME Mesh time in my simulation. The
following is my time accounting. I am running my simulation on 2 nodes.
Each of them has 16 CPUs and 1 Tesla K20m Nvidia GPU.
And my mdrun command is ibrun
/work/03002/yliu120/gromacs-5/bin/mdrun_mpi -pin on
Please reply.
Reposting the same query again:
I have read few papers that determine transition temperature from the plot
of average MSD of hydrogen atoms of protein versus temperature. My question
is:
At a particular temperature, we get a linear curve for MSD versus time, is
it reasonable to calc
One of my friends have posted the same query earlier but hasn't got any
reply. Now, I am also having the same doubt and so posting the question on
behalf of both of us:
We would like to calculate both distance and angle water orientational
order. We have made an index file containing all oxygen at
