Dear Dr. Spoel,
Initially I used a 100ns simulation with 0.002 time step.
Then I tried a 10ns simulation with 0.0005 timestep and lower output
frequency.
I used -ac option and obtained the forward lifetime.
Regards,
Apramita
Reply to :Message: 2
Date: Fri, 7 Sep 2018 08:14:48 +0200
From:
On Fri, Sep 7, 2018 at 4:15 PM Benson Muite wrote:
> Check if the routines you will use have been ported to use GPUs. Time
> and profile a typical run you will perform on your current hardware to
> determine the bottlenecks, and then choose hardware that will perform
> best on these bottlenecks
Hi,
A lot of thanks for valuable information.
If it isn’t difficult for you, could you answer how the growth of
performance under using the second GPU on the single simulation was changed
in GROMACS 2018 vs older versions (2016, 5.1, it was 20-30% higher)?
2018-09-07 23:25 GMT+07:00 Szilárd Páll
Hi,
Are you intending to use it mostly/only for running simulations or also as
a desktop computer?
Starting with the 2018 release we offload more work to the GPU to account
for the increase in the gap between the performance of CPUs and GPUs and
the prevalence of (especially workstations) with
Check if the routines you will use have been ported to use GPUs. Time
and profile a typical run you will perform on your current hardware to
determine the bottlenecks, and then choose hardware that will perform
best on these bottlenecks and is within your budget.
Note that benchmarking can be
Dear All,
In my simulations ,I have a Peptide in aqueous solution with a cosolvent.
I'm trying to calculate the forward hydrogen bond lifetime with g_hbond and
-ac flag.
For more number of hydrogen bonds like peptide water, water-water, there
are no warnings
But for Peptide cosolvent, there are
Den 2018-09-06 kl. 17:13, skrev Apramita Chand:
Dear All,
In my simulations ,I have a Peptide in aqueous solution with a cosolvent.
For more number of hydrogen bonds like peptide water, water-water, there
are no warnings
But for Peptide cosolvent, there are 315 hydrogen bonds and it does the
Hi everyone,
I reading about the viscosity methods in the EMD by Gromacs and I have just
a simple question. In the user manual in section 6.11 there is an
explanation about the Einstein method used in the gmx energy -vis, however,
in the section 8.6.5 there is another explanation about the Green
