Okay, thank you. Majid
________________________________ From: Justin A. Lemkul <[email protected]> To: Gromacs Users' List <[email protected]> Sent: Sun, April 17, 2011 12:28:47 PM Subject: Re: [gmx-users] genbox output taking forever to complete majid hasan wrote: > Okay, so here is an output attached, for cubic box of length 10. > > Actually, the carbon atoms are all placed at 0<x<4, 0 <y< 2.5, 0<z<3.5. >While solvent and DNA atoms are in the region 4<x,y,z<6. So > Then your box size is overkill. All you're going to end up doing is adding tens of thousands of waters that do not serve any purpose for most applications. There is (in general) no need for a 4-nm buffer around your system. Take your unsolvated coordinate file and run editconf -d 1 to obtain a more suitable box before trying genbox again. > only DNA is solvated, while CNT is just lying outside. Though I might have >placed solvent in a cube of length 10 (using: editconf -f spc216.pdb -o >spc216.gro -box 10 10 10), could this be the reason? > Yes, as I said before - do not adjust the box of spc216.gro. The genbox program takes the input solvent configuration (unmodified, please!) and tiles it across the box defined in the -cp configuration such that it fills the box. If you make a solvent box with a bunch of empty space just to "fit" in your existing box, you accomplish nothing at all and genbox will probably chew up a lot of memory trying to make this exact fit. > I am at the moment trying to solvate the whole system (in a cubic box of 20) >without specifying -box in editconf -o spc216.gro, but this is taking long, >its >running for about half an hour after reaching this point: Reading solvent >configuration "Quotation" Solvent configuration contains 648 atoms in 216 >residues. Is that much time normal, I am running it on my laptop, which is 2GB >Ram, and Dual Core ~1.4GHz processor? That is an enormous box that will require a large amount of memory to accomplish. Before trying to get a huge box to work, make sure you can do something more "normal" as I suggest above. You haven't stated your overall purpose, but for only a very few particular tasks would you ever require a system this large for components as small as the ones you're dealing with. -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
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