Mengsheng Zhang

Hi Lorenzo, I'm running a system with 74 nucleotides of DNA, running on the CPU for a long time, and the program is still running. Does this structure run faster on GPU?

Hi, I have modified some of the parameters according to the suggestions you provided. If I want to obtain equilibrium result, then is the larger the number of steps, the better ? The number of steps I currently set is 2e5.

Hi, Thanks for the reply. I have a question in regards to a project that I am working on. I first got the prova.top and .conf files using oxviewer, then referred to RELAX_INITIAL_CONFIGURATION to relax structure, and then ran MD simulation. I was simulating the force-extension of nucleic acid, requiring one end to be fixed and the other end (not the end) to be applied. However, it seems that the structure obstained at last is not correct (the nucleic acid is still folding and when the force increases,...

Hi, Thanks for the reply. I have a question in regards to a project that I am working on. I first got the prova.top and .conf files using oxviewer, then referred to RELAX_INITIAL_CONFIGURATION to relax structure, and then ran MD simulation. I was simulating the force-extension of nucleic acid, requiring one end to be fixed and the other end (not the end) to be applied. However, it seems that the structure obstained at last is not correct (the nucleic acid is still folding). Could you please help...

Hi, Thanks for the reply. I have a question in regards to a project that I am working on. I first got the prova.top and .conf files using oxviewer, then referred to RELAX_INITIAL_CONFIGURATION to relax structure, and then ran MD simulation. I was simulating the force-extension of nucleic acid, requiring one end to be fixed and the other end (not the end) to be applied. However, it seems that the structure obstained at last is not correct (the nucleic acid is still folding). Could you please help...

Hi, I am new user for oxDNA and I recently want to simulate the DNA hairpin unfolding force(the force-extension curve in the attachment), In it, one end of DNA hairin is fixed and the other end is forced. Is there any way to solve this problem? Or how can I simulate it using oxDNA? Thanks! Best, Mengsheng Zhang

Hi, I am new user for oxDNA and I recently want to simulate the DNA hairpin unfolding force(the force-extension curve in the attachment), Is there any way to solve this problem? Or how can I simulate it using oxDNA? Thanks! Best, Mengsheng Zhang

I compiled it with gcc 9.4 as you suggested, this should be a successful compilation, right? Thank you for helping me solve a problem that has puzzled me for days.