Hi GMX Users,
I am writting this email, beacause I think the g_msd program in Gromacs 4.5.4
bears a problem. I was calculating the MSD od center of mass of POPC in
membrane (system contains 274 POPC lipid molecules in all-atom force field)
from 50 ns trajectory and it seems to consume great amou
600 GB of memory? I highly doubt that you have that much memory
available. Are you sure that this is not a typo? Can you please post
evidence that you have >=600 GB of memory available? It is common for
clusters to disallow an individual process from using >10% of the
total memory on a head
Hi Slawomir,
That's quite a usage of memory! Can you provide more information? Like
the number of frames in the trajectory, the command line you used, and
the system you ran on?
Cheers,
Tsjerk
2011/6/27 Sławomir Stachura :
> Hi GMX Users,
> I am writting this email, beacause I think the g_msd p
Hello,
thank you for your reply. I have used following command :
g_msd -n POPC.ndx -lateral z -o POPC_msd.xvg -mol POPC_diff.xvg
Trajectory has 1 frames and the system it was ran on is Fedora Red Hat 5.4.
Indeed my network administrator was very unhappy about comsumed memory.
Regards,
No -it is not a typo - my cluster allows me to use higher amount of memory than
10%. Information I received from administrator of the cluster :
>> [root@isei ~]#top
>>
>> top - 13:52:23 up 30 days, 3:00, 76 users, load average: 5.85, 17.19,
>> 13.08
>> Tasks: 2825 total, 1 running, 2815 sleep
On 27/06/2011 11:57 PM, Sławomir Stachura wrote:
Hello,
thank you for your reply. I have used following command :
g_msd -n POPC.ndx -lateral z -o POPC_msd.xvg -mol POPC_diff.xvg
Trajectory has 1 frames and the system it was ran on is Fedora Red Hat 5.4.
Indeed my network administrator was
Dear all,
I found the same problem that Sławomir pointed out 10 days ago about
the memory usage in the computation of g_msd.
I have 100 ns simulation for 2880 water molecules. The trajectory is
savede every 1 ps: this means that I have 10 frame
I think that there is a strange memory p
Hello,
I can also confirm this behaviour. Furthermore if I use an index group,
that just contains 1 molecule and compare the results from an analysis
with the flag -mol and without, then I obtain different results which
should not be the case.
/Flo
On Thu, 2011-07-07 at 09:28 +0200, Ivan Gladic
Dommert Florian wrote:
Hello,
I can also confirm this behaviour. Furthermore if I use an index group,
that just contains 1 molecule and compare the results from an analysis
with the flag -mol and without, then I obtain different results which
should not be the case.
It sounds like it's time
I just experienced this myself. The problem appeared to manifest
itself when I was using -mol on a molecule that straddled the box
wall. Memory usage was extremely high and the resulting MSD plot did
not show any linear behavior. Imaging the trajectory with -pbc nojump
made g_msd's memory usage
Thank you for all your answers. It reassures me that the problem I encountered
wasn't only a secluded case.
I can also confirm that the -mol options seems to be the one making the most
consumption of the resources - without it memory usage has dropped to 20 gb.
And it could be connected to dealin
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