Re: [gmx-users] Error in production run

Hi Justin, Thanks. I will have a look at this link. On Thu, Jun 14, 2012 at 12:27 AM, Justin A. Lemkul wrote: > > > On 6/13/12 12:21 PM, Malai wrote: > >> Hi, >> >> Can you suggest me what went wrong in my production run . I got the >> following

[gmx-users] Error in production run

Hi, Can you suggest me what went wrong in my production run . I got the following error that stopped my run. Thanks. --- Program mdrun_mpi, VERSION 4.5.4 Source code file: domdec.c, line: 2861 Fatal error: The X-size of the box (6.311743) times

Re: [gmx-users] input/output error in production grompp

HI Justin, I did use the .pdb file as I showed in the grompp command. If I got I/O error, the mdrun should not work? but here the mdrun is working. Thanks. On Wed, Jun 13, 2012 at 9:14 PM, Justin A. Lemkul wrote: > > > On 6/13/12 9:11 AM, Malai wrote: > >> Hello Justin, >

Re: [gmx-users] input/output error in production grompp

Hello Justin, Thanks for reply. After getting this, I started to run production run but here i didnt get any error. so is it OK? or still I need to look at this error? Thanks On Wed, Jun 13, 2012 at 8:35 PM, Justin A. Lemkul wrote: > > > On 6/13/12 8:27 AM, Malai wrote: > >&g

Re: [gmx-users] input/output error in production grompp

troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors> Thanks. On Wed, Jun 13, 2012 at 7:52 PM, Justin A. Lemkul wrote: > > > On 6/13/12 7:36 AM, Malai wrote: > >> Hi, >> >> I us

[gmx-users] input/output error in production grompp

Source code file: futil.c, line: 491 File input/output error: hex1.gro For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Many Thanks. Malai -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Error in grompp steps of position restrained

ks. > > > http://www.gromacs.org/Documentation/File_Formats/Index_File > so i need to make index files for CA atoms of protein using make_ndx for CA. can you please explain how to make index file for CA using make_ndx. Thanks for help. > > Mark > > > On Fri, Jun 8, 2012

Re: [gmx-users] Error in grompp steps of position restrained

Dear Mark, Thanks for mail. you mean I need to define in mdp file?. Can you please guide me how to do that. Thanks. On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham wrote: > On 8/06/2012 12:23 PM, Malai wrote: > >> Hi, >> >> After Successfully neutralizing and sd minimizat

[gmx-users] Error in grompp steps of position restrained

Hi, After Successfully neutralizing and sd minimization of the system, I got the below error when I try the grompp for position restrained step. The command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o complx_eqn1.tpr Any help will be highly appreciated. Many thanks. Erro