On 1/17/20 7:12 AM, ZHANG Cheng wrote:
Many thanks for Justin's advice forassigning the same number of PP and PME ranks in
each run (30/6 in 5.1.1 and 27/9 in 2019.3). Sorry I am not familiar with these kind of
settings, can I ask how to do this exactly? e.g. how to change "gmx mdrun
Many thanks for Justin's advice forassigning the same number of PP and
PME ranks in each run (30/6 in 5.1.1 and 27/9 in 2019.3). Sorry I am not
familiar with these kind of settings, can I ask how to do this exactly? e.g.
how to change "gmx mdrun -deffnm md_0_1 -cpi -append" ?
He said he ran a nearly identical simulation on two versions of gromacs but
I didn't think so,
in 2019.3 logs:
There are: 117860 Atoms
Atom distribution over 27 domains: av 4365 stddev 75 min 4289 max 4626
and 5.1 logs:
There are: 127790 Atoms
Atom distribution over 30 domains: av 4259 stddev 90
On 1/16/20 11:57 AM, ZHANG Cheng wrote:
I have re-run the MD, with only 2 ps in both version. Indeed, the Version 2019
is far slower than the Version 5.1.1.
Version 2019 needs 114.111 hours to complete 1 ns, while Version 5.1.1 only
needs6.362 hours to complete 1 ns.
The new logs files
I have re-run the MD, with only 2 ps in both version. Indeed, the Version 2019
is far slower than the Version 5.1.1.
Version 2019 needs 114.111 hours to complete 1 ns, while Version 5.1.1 only
needs6.362 hours to complete 1 ns.
The new logs files are at
On 1/15/20 6:58 PM, ZHANG Cheng wrote:
Hi Justin, what kind of information should I look at in the log files? They are too big
to paste here. Would it be possible if you can see them
athttps://github.com/lanselibai/gromacs-20200115;?
It doesn't look like either of those runs actually
Hi Justin, what kind of information should I look at in the log files? They are
too big to paste here. Would it be possible if you can see them
athttps://github.com/lanselibai/gromacs-20200115;?
Thank you!
--Original--
From:"ZHANG Cheng"<272699...@qq.com;
On 1/15/20 2:38 PM, ZHANG Cheng wrote:
I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the
preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro"
and "-r npt.gro" are
I have a nearly identical run using the "VERSION 2019.3" compared to my
previous "VERSION 5.1.1". Everything during the preparation is the same except
"-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro"
and "-r npt.gro" are added in the grompp commands for NVT, NPT and
