Thanks..You are right...The last line of gro file says 250 so it is in nm!...
On 10 October 2012 12:30, Christopher Neale <[email protected]> wrote: > Sounds like you ran out of memory. Many clusters have a few large-memory > nodes. Can you use one of those? > It's failing on a call for 1.3 Gb of memory, which by itself isn't really a > lot... > > Also, can you confirm 250 A box length, not 250 nm box length? Gromacs > defines length in units of nm. > > Chris. > > -- original message -- > > I am trying to build a polymer in solvent system by solvating my fully > extended polymer chains in a box of size 250 250 250 A. I am adding > 4500 solvent molecules as below > > genbox -cp Solute.gro -ci solvent.gro -o solvated.gro -nmol 4500 > > Adding solvents is a slow process and takes much time and at the end I get: > > Program genbox, VERSION 4.5.4 > Source code file: smalloc.c, line: 214 > > Fatal error: > Not enough memory. Failed to realloc 1338273212 bytes for grid->nra, > grid->nra=0x0 > (called from file nsgrid.c, line 483) > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > Is this happening because of the huge amount of free space to be > filled with the solvent? Please help me. > -- > Thanks, > -- > 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 -- Thanks, J. N. -- 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
