Hi, I will try to compress before doing genbox. As for the number of atoms, as I said I *dont *intend to fill up the whole box with solvent. So I put around 4000 solvent molecules to get the desired polymer Wt%, hence there would be a lot of free space for a total of 120 000 atoms approx..Also I tried - cs solvent.gro but it stucks and doest work.
Thanks for the comments, J. On 10 October 2012 17:16, Dr. Vitaly Chaban <[email protected]> wrote: > 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 <[email protected]> wrote: >> 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 >> -- 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
