Re: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space

On 4/26/14, 8:42 AM, Andrew Bostick wrote: Dear Justin Thanks for your reply. This problem can be solved by changing the parameters related to file system ? Well, you could, but that would require reformatting your file system for something that can handle file size > 2 GB. If I add

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Justin Thanks for your reply. This problem can be solved by changing the parameters related to file system ? If I add another RAM to my computer system, my problem solves? Best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing

Re: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space

On 4/26/14, 4:54 AM, Andrew Bostick wrote: Dear Mark I'm apologize. You are right. I should give more indication and information you to help me. I used chmod -R 777 directory containing pdb and mdp files. Then I did MD simulation again: (pdb2gmx ...> editconf > em ...> npt eq ...> m

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Mark I'm apologize. You are right. I should give more indication and information you to help me. I used chmod -R 777 directory containing pdb and mdp files. Then I did MD simulation again: (pdb2gmx ...> editconf > em ...> npt eq ...> md) My problem is in md step (md.trr file). 1)

Re: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space

You've been reading a bit selectively. I asked if you're trajectories wrote any output at all, but you haven't said. If, as I've already said, you know you were able to write output because gmxcheck says there's content in the files, then a flaky network file system is likely. But you haven't given

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Mark I corrected file permission in my system using chmod -R 777 . But I encountered the same error: File input/output error: Cannot write trajectory frame; maybe you are out of disk space. Any help will highly appreciated -- Gromacs Users mailing list * Please search the archive at htt

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Mark Thanks for your reply. I googled file permission in linux OS. After that I did following steps: I created a directory entitled input. I put pdb and mdp files in the input directory. I used following command to change permission: chmod -R 777 input Now I will md simulation steps (pd

Re: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Did earlier frames get written? Use ls -l, gmxcheck etc. Google about file permissions - unlike on (say) an old Windows machine, on a compute cluster you will not be able to write files anywhere but where you're allowed to. Guessing here, because you haven't supplied any context. Mark On Mon, Ap

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Mark Thanks for your reply. I am beginner in linux and gromacs. How to rule out file permissions issues? Which command is true for doing this? Please guide me to solve this problem. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_List

Re: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space

If you can rule out file permissions issues (because you wrote files earlier), and actually running out of disk, usually that would suggest a flaky network file system. Mark On Mon, Apr 21, 2014 at 4:09 PM, Andrew Bostick wrote: > Dear gromacs users > > I am doing md simulation on the a protein

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear gromacs users I am doing md simulation on the a protein with 190 residues. I did minimization and equilibration without problem and error. But in production run step (last md simulation with 1500 steps), in step 650, I encountered with following error: File input/output error: Cann

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space?

dear all, i am getting following error on giving command for NVT equilibrations: mdrun -deffnm nvt -v -nt 8 File input/output error: Cannot write trajectory frame; maybe you are out of disk space? i have gromacs 4.6.4 version, 12.04 ubuntu, 7.9GiB memory and 976 GB Disk space, i am simulat

Re: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space?

Run somewhere where you have write permissions, like your home directory. Don't run in root file space, or as root! Mark On Nov 18, 2013 1:04 PM, "vansh" wrote: > dear all, > i am getting following error on giving command: mdrun -deffnm nvt -v -nt 8 > File input/output error: > Cannot write tra

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space?

dear all, i am getting following error on giving command: mdrun -deffnm nvt -v -nt 8 File input/output error: Cannot write trajectory frame; maybe you are out of disk space? i have gromacs 4.6.4 version, 12.04 ubuntu, 7.9GiB memory and 976 GB Disk space, i am simulating 414aa long protein for 10n