By the way, if you place your solvent molecule (-cs ____.gro) into a very large box, such as 10x10x10nm, genbox may perform well. I did NOT try, just an idea.
For the overall system setup, I would rather follow the previous comments anyway. On Wed, Oct 10, 2012 at 10:49 PM, Dr. Vitaly Chaban <vvcha...@gmail.com> wrote: > On Wed, Oct 10, 2012 at 10:24 PM, Juliette N. <joojoojo...@gmail.com> wrote: >> 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. > > > Sorry, I do not believe you. 120 000 atoms cannot ever fill the volume > of 250*250*250 nm^3. > > >> 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.? > > This "adding memory" is the appetit of the genbox in its current > incarnation. I am sure that the developers did not expect to apply > this utility for the systems larger than 30x30x30 nm. You can always > construct a very simple script that puts your solvent evenly > throughout the box. > > Why not to gently compress the box WITHOUT solvent..... Unless you > want to observe real-time folding of the polymer. It is probably not > so good idea to start with a huge box and super low density. > > > 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 > > > > > > >> 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
