Yes, you are right. I made a mistake to write an error: [n0017:07436] *** Process received signal *** [n0017:07436] Signal: Segmentation fault (11) [n0017:07436] Signal code: Address not mapped (1) [n0017:07436] Failing at address: 0x1d620d20
What do you mean for "Better energy minimization"? Thanks, Dariush On Wed, Mar 14, 2012 at 10:08 AM, Justin A. Lemkul <[email protected]> wrote: > > > Dariush Mohammadyani wrote: > >> Dear user, >> When I am using: >> genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro >> to add water in a coarse grained system, after running mdrun I am >> getting "Syntax error" and it shows maybe the distances are so close or >> there are some clashes. >> >> > > I've never heard of mdrun throwing a syntax error. Can you please copy > and paste the complete error message from your terminal? > > > Do you know how can I figure it out? >> Or actually if we have some clashes in system how we can correct them? >> >> > > Better energy minimization typically solves bad atomic clashes. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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> >
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