On Wed, Oct 10, 2012 at 10:24 PM, Juliette N. <[email protected]> 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 <[email protected]> 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 >>> <[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. >> >> >> 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 [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_Lis -- 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
