Dear Justin, Thank you for your help, however, the problem was originated from absence of -table table_d1.xvg flag in my mdrun command. Now it is fixed.
BR Arman On Sat, Oct 13, 2012 at 10:30 PM, Justin Lemkul <[email protected]> wrote: > > > On 10/13/12 9:49 AM, Arman Mahboubi Soufiani wrote: > >> Dear Justin, >> >> The followings are the two successive commands I used: >> >> *grompp -f justPLA.mdp -c 20LA-2layer-4chains.gro -p t-PLA.top -o >> justPLA-em.tpr >> >> mdrun -deffnm justPLa-em* >> >> > These commands would not produce the error posted previously. The error > would have resulted from: > > mdrun -deffnm justPLA-em.tpr > > The fact that the capitalization is different and the nature of the suffix > supports this conclusion. It is better to copy directly from the terminal > rather than try to recreate what you did. In any case, proper invocation > of the command should solve the issue. mdrun is looking for an .xvg file > containing parameters for a tabulated dihedral; it needs to be named > appropriately to function correctly. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
