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

[gmx-users] out of disk space error

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