Choosing appropriate output-frequency settings, nsteps to cap your file
size, and mdrun -noappend is likely your best approach.
Mark
On Wed, Jun 4, 2014 at 8:54 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Tue, Jun 3, 2014 at 10:35 PM, Carlos Familia carlosfami...@gmail.com
wrote:
i had a same type of problem when i was using gromacs 4.6.4 version ..
the problem was with 32 bit system..when i changed to 64 bit operating
system evrything went on fine.
but in my case i was getting same error (disk space error) after 2.2 gb
file was generated although i had 800 gb free
Hi Pavan,
When you use the grompp command to prepare the md.tpr file for the final
mdrun, do you notice such a statement This run will generate roughly X
Mb of data. I suspect the resultant trajectory could be exceeding the
available space.
On Tue, Mar 4, 2014 at 4:12 PM, Pavan Kumar
...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Pavan Kumar
kumar.pavan...@gmail.com
Sent: 04 March 2014 09:38
To: gmx-users
Subject: Re: [gmx-users] Out of Disk Space
Hello THOMMAS,
Exactly, it showed 2.2GB of trajectory is going to be created.
But i have 17GB
I have executed for two times, each time i get different error.
And you got *different* errors... What's the difference?
Did you get the error at exactly the same integration time-step?
Did you try to resproduce the error on another disk partition?
Dr. Vitaly V. Chaban
--
Gromacs Users
On 12/4/13 5:24 AM, a...@imtech.res.in wrote:
I think so. You are outputting the information too often i.e every 0.2
ps i.e. 5000 times per ns. See this thread
http://comments.gmane.org/gmane.science.biology.gromacs.user/32721
It is unlikely that a few hundred ps of NVT would fill up
If none of the earlier suggestions worked then, it could be a simple
problem of power port from which you have connected your hard disk. Try
reconnecting the hard disk and and retry running the mdrun.
Posting the exact commands used while writing the output during mdrun, may
help to trace the
hi chandan..
output for ls -1 is as follows:
the directory from where i am running simulatons is in desktop .. and i have
all the permissions for it. i am not that used to ubuntu and your suggestion
will be of great help ..
total 52
drwxrwxrwx 9 vansh vansh 4096 Nov 22 14:40 Desktop
drwxr-xr-x 2
Dear vaani,
Please rerun the gmx executable.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Wed, Dec 4, 2013 at 11:20 AM, vaani vsha...@imtech.res.in wrote:
hi chandan..
output for ls -1 is as follows:
the directory from where i am running simulatons is in desktop .. and i
have
Dear vaani,
Sorry for the unclear message. Try running the mdrun command once again and
post the out put of the log file.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Wed, Dec 4, 2013 at 12:34 PM, vaani vsha...@imtech.res.in wrote:
i am sorry ..but i kind of dint get you ..
-
sure ..
-
thanks in advance :)
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View this message in context:
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Gromacs Users mailing list
* Please search the archive at
vaani wrote nvt.log
http://gromacs.5086.x6.nabble.com/file/n5013030/nvt.log
find the attached nvt.log file ..
i have been equilibrating for 200ps in this example..and getting this error
,
but when equilibrating for 100ps there is no such error ..in later case i am
getting this error at the
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