Hi everyone!
I have some problem with VMD
after finishing NAMD, because of disrupting during running, Now I have 5 dcd files (102 GB)
but when I tried to upload them in VMD, it was crushed and the VMD was closed when it reached to 1200 frames.
Now! what should I do!?
the catdcd can help solving this problem ? if yes please help me in detail and simply because I am new in VMD and NAMD :(
I came across this problem too as the CPU of the computer couldn't run those files and then interrupted. So I had to change settings so that the VMD would load half of them alternately. To do so, you can follow this:
VMD > VMD main window > Molecule file browser: Frames: strides: change 1 to 2
Hi, the option provided by Enayat is good, use stride (skip some frames while loading). However, there might be another issue as well. What type of OS are you on, how much RAM? Windows version of VMD is 32bit application (except the specific recent alpha versions 1.9.4) that cannot use more than some few GB of RAM, so if you try to import very large dcd trajectory it crashes (despite having hign amounts of free RAM). I found a good solution to remove explicit water, which decreases the file substentially, or try the 64bit version of VMD. On Linux RAM should not pose a problem for loading, yet if the file is 100gb and you do not have enough RAM it might just crash either way.
I would also suggest to change the stride value as mentioned by Enayat Mohsenzadeh. You can try with even larger stride value (10 or 20) based on how much RAM is available on the machine. If you have ~10GB RAM, you can probably load one tenth of the trajectory. So, try loading every 10th frame instead using a stride value of 10.
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