Hi,
I did by "gmx gangle ..." command. But I am not getting good result,
because I have a doubt in ndx file. Can you help me for making ndx file.
How should I select the atom for vectors.
Thanks
On Mon, Jul 29, 2019, 22:50 David van der Spoel
wrote:
> Den 2019-07-29 kl. 18:26, skrev Omkar
Den 2019-07-29 kl. 18:26, skrev Omkar Singh:
Hi,
Meaning is that If I want to calculate angle between OH, HH and dip vector
with positive Z-axis. How can I make index file for this issue? And is it
possible that the angle distribution of these vectors for bulk water
aproximatly linear. Hope now
Dear all,
These days I want to use cvff force field but in gromacs there is no relative
files for it. So I want to know if I can add it and how to make it.
Thanks sincerely,
YiLu
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Hi,
Meaning is that If I want to calculate angle between OH, HH and dip vector
with positive Z-axis. How can I make index file for this issue? And is it
possible that the angle distribution of these vectors for bulk water
aproximatly linear. Hope now question is clear.
Thanks
On Mon, Jul 29,
Hi,
Yes and the -nmpi I copied from Carlos's post is ineffective - use -ntmpi
Mark
On Mon., 29 Jul. 2019, 15:15 Justin Lemkul, wrote:
>
>
> On 7/29/19 8:46 AM, Carlos Navarro wrote:
> > Hi Mark,
> > I tried that before, but unfortunately in that case (removing —gres=gpu:1
> > and including
Carlos,
You can accomplish the same using the multi-simulation feature of
mdrun and avoid having to manually manage the placement of runs, e.g.
instead of the above you just write
gmx mdrun_mpi -np N -multidir $WORKDIR1 $WORKDIR2 $WORKDIR3 ...
For more details see
Thank you
On Mon 29 Jul, 2019, 6:45 PM Justin Lemkul, wrote:
>
>
> On 7/29/19 7:55 AM, Bratin Kumar Das wrote:
> > Hi Szilard,
> > Thank you for your reply. I rectified as you said. For
> trial
> > purpose i took 8 nodes or 16 nodes... (-np 8) to text whether it is
> running
> >
On 7/29/19 7:55 AM, Bratin Kumar Das wrote:
Hi Szilard,
Thank you for your reply. I rectified as you said. For trial
purpose i took 8 nodes or 16 nodes... (-np 8) to text whether it is running
or not. I gave the following command to run remd
*mpirun -np 8 gmx_mpi_d mdrun -v
On 7/29/19 8:46 AM, Carlos Navarro wrote:
Hi Mark,
I tried that before, but unfortunately in that case (removing —gres=gpu:1
and including in each line the -gpu_id flag) for some reason the jobs are
run one at a time (one after the other), so I can’t use properly the whole
node.
You need to
On 7/29/19 3:24 AM, m g wrote:
Dear all, I'm simulating a MOF by UFF force field, but in energy minimization step I gave an
error as "Steepest Descents converged to machine precision in 2115 steps, but did not
reach the requested Fmax < 1000", although the potential energy was converged. I
Hi Mark,
I tried that before, but unfortunately in that case (removing —gres=gpu:1
and including in each line the -gpu_id flag) for some reason the jobs are
run one at a time (one after the other), so I can’t use properly the whole
node.
——
Carlos Navarro Retamal
Bioinformatic Engineering.
Hi Szilard,
Thank you for your reply. I rectified as you said. For trial
purpose i took 8 nodes or 16 nodes... (-np 8) to text whether it is running
or not. I gave the following command to run remd
*mpirun -np 8 gmx_mpi_d mdrun -v -multi 8 -replex 1000 -deffnm remd*
After giving the
Den 2019-07-29 kl. 12:24, skrev Omkar Singh:
Hello everyone,
Is it possible that the probability distribution of HH, OH vector for bulk
water is approximately linear?
What do you mean?
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala
Hello everyone,
Is it possible that the probability distribution of HH, OH vector for bulk
water is approximately linear?
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Hi,
When you use
DO_PARALLEL=" srun --exclusive -n 1 --gres=gpu:1 "
then the environment seems to make sure only one GPU is visible. (The log
files report only finding one GPU.) But it's probably the same GPU in each
case, with three remaining idle. I would suggest not using --gres unless
you
Hi Szilárd,
To answer your questions:
**are you trying to run multiple simulations concurrently on the same
node or are you trying to strong-scale?
I'm trying to run multiple simulations on the same node at the same time.
** what are you simulating?
Regular and CompEl simulations
** can you
Dear all, I'm simulating a MOF by UFF force field, but in energy minimization
step I gave an error as "Steepest Descents converged to machine precision in
2115 steps, but did not reach the requested Fmax < 1000", although the
potential energy was converged. I used SPC/E water for this system.
Den 2019-07-29 kl. 04:24, skrev Maryam:
Dear all,
I want to apply a space but not time dependent electric field to my system.
I reviewed the source code of the electric field but it only has constant
and time dependent EF (pulsed EF). Can anyone help me find out how I can
change the source code
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