Hi
*gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c* I have used the above command to generate the box. Infact I have used this command before and I never got any error. Thank you On Mon, Nov 27, 2017 at 7:07 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/27/17 7:17 AM, RAHUL SURESH wrote: > >> Dear Users >> >> I am trying to carryout protein-metal interaction using charmm36 ff. >> During >> solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o >> solv.gro" >> *i receive a error stating >> >> >> >> >> >> >> >> >> *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for >> atoms_->atom,atoms_->atom=0(called from >> file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/ >> topology/atomsbuilder.cpp,line >> 86)". * >> I have enough space to carry out this simulation and I am using 2016 >> version of gromacs. >> > > How large is your box? Are you sure you have set its size in nm, not A? > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
