Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi, I can check all the possible combinations you listed in http://redmine.gromacs.org/issues/1834. Since my programming capability is limited, please direct me how to proceed for solving this issue? On Tue, Oct 6, 2015 at 9:00 PM, Teemu Murtola wrote: > Thanks for the clarification. I updated t

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Thanks for the clarification. I updated the Redmine issue ( http://redmine.gromacs.org/issues/1834) with a summary and next steps. I unfortunately do not have access to various systems to test the issue, but I put some guesses on the possible reasons in the issue. Best regards, Teemu On Tue, Oct

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi, Sorry for the confusion. Now I have generated a small xtc file and a very big pdb file. I can able to access small xtc file but unable to read the large pdb file (~10GB) (terminating with the same error as reported earlier). Does it mean my installation has some problem? On Mon, Oct 5, 2015 at

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi, That unfortunately doesn't tell us anything, since 1.5GB can still be read with 32-bit file operations. You didn't answer any of the questions: can you open very small xtc files, or very large (requiring 64-bit access) gro/pdb files, or not? We are still thinking that you should be able to ope

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi, Sorry for the delay in reply. I am able to access pdb/gro files of size 1.5 GB with Gromacs-5.1 version. My Desktop is 32-bit whereas my xtc files were generated on our super cluster, which runs on 64-bit O.S. On Fri, Oct 2, 2015 at 9:46 AM, Teemu Murtola wrote: > Hi, > > On Thu, Oct 1, 2015

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi, On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll wrote: > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy wrote: > > Gromacs-5.1 version can not read xtc files. However, it can access single > > frame gro/pdb files. > > > > That's a bold claim that IMO requires equally strong proof. > I agree with

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy wrote: > Hi > Gromacs-5.1 version can not read xtc files. However, it can access single > frame gro/pdb files. > That's a bold claim that IMO requires equally strong proof. In your other mail to the list you were talking about a 32-bit Ubuntu VM. Are

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi Gromacs-5.1 version can not read xtc files. However, it can access single frame gro/pdb files. On Thu, Oct 1, 2015 at 10:44 AM, Teemu Murtola wrote: > Are you saying that you cannot open any xtc files? If that is the case, > then this may not have anything to do with 64-bit for support. Can

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Are you saying that you cannot open any xtc files? If that is the case, then this may not have anything to do with 64-bit for support. Can your Gromacs compilation open any files? You will need to isolate the problem a bit to help diagnosing it, since we don't have access to your system. Teemu On

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi, 1) Yes, I can access the same xtc with older gromacs versions. 2) I can't access even smaller xtc files with 5.1 I will file a bug report for the same. Thank you On Wed, Sep 30, 2015 at 9:28 PM, Teemu Murtola wrote: > Hi, > > This sounds like the build system is not compiling Gromacs with

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi, This sounds like the build system is not compiling Gromacs with 64-bit file support like it should. Can you access the same file on the same system with earlier Gromacs versions? Can you access smaller files with 5.1? Could you file a bug report at redmine.gromacs.org, and include at least th

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi Teemu, Thanks for the prompt reply. Yes, the xtc file size is larger than 2GB (approx. 50GB) and both system.xtc and traj.xtc are same files. I am extremely sorry for the confusion :) On Wed, Sep 30, 2015 at 11:31 AM, Teemu Murtola wrote: > Thanks for testing it, I see that there is still roo

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Thanks for testing it, I see that there is still room for improvement in getting more context information into the error messages. I'm a bit confused by the difference between your original report of system.xtc vs traj.xtc in the new message, but that may not matter that much. Is your xtc file larg

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi Teemu, Thank you for providing the patch. But the patched version is giving following error message: Program: gmx rdf, VERSION 5.2-dev Source file: src/gromacs/utility/path.cpp (line 406) Function:static void gmx::File::throwOnError(const gmx::File::NotFoundInfo&) System I/O error: Fai

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi, I now changed the check to provide more details (in 5140 ). If you haven't figured out what the issue was, you could try building the source code from the above link, and running it to get more details. There is not much we can do to help diagnose the issue fu

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

This error has nothing to do with the contents of the file, but rather the operating system appears to be telling Gromacs that the file cannot be opened or that it is not a regular file. With the information here, it's difficult to say anything more; if you want to debug this further, the relevant

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi Tsjerk, Thank you for the quick reply. Yes I can access it with other versions, like 4.5.5, 5.0.4. On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar wrote: > Hi Venkat, > > Does it exist? Is it accessible? The XTC format did not change since the > early years of Gromacs. Can you access it wi

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi Venkat, Does it exist? Is it accessible? The XTC format did not change since the early years of Gromacs. Can you access it with a different version? Cheers, Tsjerk On Sep 25, 2015 19:52, "Venkat Reddy" wrote: > Dear all, > I have a trajectory file generated by gromacs-4.5.5. Recently I trie

[gmx-users] Analysis of old xtc file using gromacs-5 tools

Dear all, I have a trajectory file generated by gromacs-4.5.5. Recently I tried to plot radial distribution function using 'gmx rdf' tool available in gromacs-5.1. But I am getting the following error. Error in user input: Invalid command-line options In command-line option -f File 'system.xt