Re: [gmx-users] Out of disk space

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 wrote: > > > > On Tue, Jun 3, 2014 at 10:35 PM, Carlos Familia > wrote: > >> Hello, >> >> I was running the final e

Re: [gmx-users] Out of disk space

On Tue, Jun 3, 2014 at 10:35 PM, Carlos Familia wrote: > Hello, > > I was running the final equilibration step (NTP) and i received an error > saying that i was running out of disk space, the trajectory file writen has > 2GB, and every retry will generate a file with the same size. I have looked

Re: [gmx-users] Out of Disk Space

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 space.

Re: [gmx-users] Out of Disk Space

>> > 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 U

Re: [gmx-users] Out of Disk Space

...@maillist.sys.kth.se on behalf of Pavan Kumar 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 of free space on my cluster on which i am running. So any other reasons for

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 of free space on my cluster on which i am running. So any other reasons for the error. Thanks in advance. On Tue, Mar 4, 2014 at 8:00 PM, MUSYOKA THOMMAS < mutemibiochemis...@gmail.com> wrote: > Hi Pav

Re: [gmx-users] Out of Disk Space

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 wrote:

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

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 prob

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

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

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

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 some

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

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 Amin. On 2013-12-04 15:11, vaani wrote: > hi .. > thanks for the reply.. > but does it has to do something

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

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-

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

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 > > - > t

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

vaani wrote > 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

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

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 U

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

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.gro

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

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 wrote: > i am sorry ..but i kind of dint get you .. > > - > thanks in advanc

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

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 se

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

Dear vaani, Please rerun the gmx executable. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Dec 4, 2013 at 11:20 AM, vaani wrote: > 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 permissi

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

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

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

Dear vaani, Please check you have sufficient permission on the disk where you are trying. Try rerunning mdrun. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Dec 4, 2013 at 10:33 AM, vaani wrote: > hello all, > i have been trying to simulate this 414 aa long protein for 10ns,us