Re: [gmx-users] Restarting a crashed run

[vaani]

hi ..i am having same problem as you did..can you please suggest how you
solved it ???


-
thanks in advance :)
--
View this message in context: 
http://gromacs.5086.x6.nabble.com/Re-Restarting-a-crashed-run-tp4456957p5013569.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] out of disk space error

[vaani]

On 12/4/13 5:24 AM, amin@.res 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 someone's disk if
it 
has several hundred GB available, but it can't hurt to reduce the output a
bit. 
  Frequent writing could be taxing the filesystem unnecessarily.

It is also important to keep in mind that some desktop computers simply
cannot 
handle a simulation that would be best run on a cluster with
high-performance I/O.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

hi justin,
i have already run simulations on this work station before also without any
such disk space problem. i am facing this problem now only after installing
ubuntu and gromacs freshly, 

best




-
thanks in advance :)
--
View this message in context: 
http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013086.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] out of disk space error

[vaani]

hi ..
thanks for the reply..
but does  it has to do something with disk space error ??



amin wrote
> Hi. You can probably try to increase the values of nstxout, nstvout,
> nstcalcenergy, nstenergy etc. to something like 2000 or 5000 and rerun.
> 100 seems very small. 
> 
> Amin. 
> 
> On 2013-12-04 12:58, vaani wrote: 
> 
>> nvt.log <http://gromacs.5086.x6.nabble.com/file/n5013030/nvt.log
>> [1]> 
>> 
>> -
>> thanks in advance :)
>> --
>> View this message in context:
>> http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013030.html
>> [2]
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> 
>  
> 
> Links:
> --
> [1] http://gromacs.5086.x6.nabble.com/file/n5013030/nvt.log
> [2]
> http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013030.html
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to 

> gmx-users-request@

> .



-
thanks in advance :)
--
View this message in context: 
http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013038.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] out of disk space error

[vaani]

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 time of 10 ns dynamic run 

-
thanks in advance :)
--
View this message in context: 
http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013032.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] out of disk space error

[vaani]

nvt.log   






-
thanks in advance :)
--
View this message in context: 
http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013030.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] out of disk space error

[vaani]

sure ..

-
thanks in advance :)
--
View this message in context: 
http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013029.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] out of disk space error

[vaani]

i am sorry ..but i kind of dint get you ..

-
thanks in advance :)
--
View this message in context: 
http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013027.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] out of disk space error

[vaani]

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 vansh vansh 4096 Nov 26 15:13 Documents
drwxr-xr-x 8 vansh vansh 4096 Dec  3 16:43 Downloads
-rw-r--r-- 1 vansh vansh 8445 Nov 12 10:03 examples.desktop
-rw-rw-r-- 1 vansh vansh 5083 Dec  3 11:20 md.log
drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Music
drwxr-xr-x 2 vansh vansh 4096 Nov 13 22:49 Pictures
drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Public
drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Templates
drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Videos


-
thanks in advance :)
--
View this message in context: 
http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013023.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] out of disk space error

[vaani]

hello all,
i have been trying to simulate this 414 aa long protein for 10ns,using
gromacs 4.6.4 version,  but at the time of mdrun i am getting this error :
file input/output error:
can not write trajectory frame ; may be you are out of disk space??
reducing time of equilibration does not give this error ..i already have 1
TB space and and approx. 870 GB is free ..i tried running as a root also but
of no use ..
any help ??

regards 


-
thanks in advance :)
--
View this message in context: 
http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.