September 2013 - Rnatoolbox-help - SimTK Mailing Lists

MMB to quad-core computer
by Vasiliki E. Fadouloglou 26 Sep '13

26 Sep '13

Dear Dr Flores, I use MMB 2.13 in a quad-core computer (8GB RAM) and Ubuntu 13.04 64bit for folding an RNA. However, the job uses just one of the four available cores. I am wondering if I could share it to all four of them. Just one more question. There is the possibility to incorporate counterions and/or water in the calculations? Many thanks. Vasiliki ---------------------------------------------------------------- This message was sent using IMBB - WebMail.

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Re: MMB to quad-core computer
by Samuel Flores 25 Sep '13

25 Sep '13

kalispera Vasili, What forum did you post your question on? I would like to answer on there but I can't find it. To answer, MMB is currently still a single-processor code. You will unfortunately get no speedup from using a quad core machine. I can perhaps provide advice on how to speed up your calculation though. You will want to reduce degrees of freedom, and make sure you have no fast oscillations in your system that might force a small time step size. Let me know if you want help with this. Sam > Hello sam, > > The following is an e-mail sent to you by fadoulog via your account on > "Simtk.org Forums". If this message is spam, contains abusive or other > comments you find offensive please contact the webmaster of the board at > the following address: > > Simtk.org Forums <noreply(a)simtk.org> > > Include this full e-mail (particularly the headers). Please note that the > reply address to this e-mail has been set to that of fadoulog. > > Message sent to you follows > ~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Dear Dr Flores, > > I use MMB 2.13 in a quad-core computer (8GB RAM) and Ubuntu 13.04 64bit for > folding an RNA. > However, the job uses just one of the four available cores. > I am wondering if I could share it to all four of them. > > Many thanks. > Vasiliki

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RNA threading problem
by UGUR UZAY Sezen 17 Sep '13

17 Sep '13

Dear MMBians, I am trying to thread around a section (nucleotides 57-91) of wheat 18S ribosomal RNA (3IZ7) using MMB_2.13. For some reason, instead of a hairpin I always get a straight helix. Strangely the target PDB file which is set rigid also becomes a linear molecule in the resulting PDB output. Can someone help me trouble shoot? I am attaching the command file, target pdb model and output pdb for you to see. Target pdb chain A: 3IZ7-57-91.pdb Command file threaded chain X: commands.3IZ7-threading-57-91.dat Result PDB: Sbi-16S-57-91 I appreciate your time and input, Uzay Sezen Uğur Uzay Sezen Post-Doctoral researcher Plant Genome Mapping Laboratory University of Georgia Center for Applied Genetic Technologies 111 Riverbend Rd., Athens, GA 30602 uzay(a)uga.edu<mailto:uzay@uga.edu> tel: 706-583-0170<tel:706-583-0170> fax: 706-583-8120<tel:706-583-8120> http://www.plantgenome.uga.edu/ http://naturedocumentaries.org/

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MMB 2.13 released
by Samuel Flores 13 Sep '13

13 Sep '13

Dear Users, I recommend upgrading to MMB 2.13. If you are using 2.12, you may encounter a bug with Physics where you want it, in which the bonded interactions are turned off. You may also note a speed improvement with 2.13. With regards, Sam

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