Hi again, The reason I have this big box is that I have fully extended chains of the length of ~ 250 nm,. In fact this 250 nm is the minimum size that I can fit the chain in the box; and I am going to fill this box with solvent and use NPT to increase the density. So I dont need to fill up the box with solvent entirely. The total number of atoms would be around 120 000.
I have access to a certain number of nodes. I am wondering if this "adding of memory" is merely a hardware issue or there is some other ways to get around this.? Thank you for your comments, On 10 October 2012 13:14, Dr. Vitaly Chaban <vvcha...@gmail.com> wrote: >> >> 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 >> <chris.ne...@mail.utoronto.ca> 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. > > > Genbox sometimes suffers from the out-of-memory error. Based on my own > investigation, this is indeed what happens here, because the utility > uses a kind of grid during its operation. The larger the cell, the > more hungry it becomes, no matter how many molecules you want to > insert. The standard advice therefore applies - add memory... > > Another question is why you need such a huge box? The only thing I > could imaging is simulating a droplet-vapor/air interface... > > Another advice is to start with a smaller box and then extend its > deminsions using editconf (which does not "care about the box size"). > > > Dr. Vitaly V. Chaban > MEMPHYS - Center for Biomembrane Physics > Department of Physics, Chemistry and Pharmacy > University of Southern Denmark > Campusvej 55, 5230 Odense M, Denmark > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Thanks, J. N. -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists