[fdd20]

Hi，

I am a newbie to simulate the LLPS using the HPS model following the tutorial . All the input files are from the tutorial, and after 10000000 steps, the FUS molecules go away from each other. And the results show the same results (Molecules go away from each other ) whether the eleele_chain_pairs is turned on or off.

 

Regards,

Devin

[ctan]

Hi Devin,

 

Can I confirm one thing, when you looked at the MD trajectory, did you consider the periodic boundary condition (PBC)? GENESIS outputs coordinates without PBC, so you have to use some tools to wrap the atoms back into the unit cell, otherwise it just looks like every molecule is going far away from each other.

 

If it’s not related to PBC, can you share more information with us? Such as the content of your MD control file, topology files for FUS, and the log file from GENESIS.

 

Best,

Cheng

[fdd20]

Dear Dr. Cheng,

Thanks a lot for your reply. I really didn’t notice the PBC and wrap all to the center before. However, I just run the command :

vmd > pbc set {180 180 1800} -all
vmd > pbc wrap -compound fragment -center origin -all

After that. nothing changed, so do I run the wrong command? If possible, could you please help me with the right parameters? And a question about the post picture. The picture posted at the end of the tutorial looks nice with every chain different color. I reproduced it by selecting all the atoms in a chain and set the color. Apparently, it is very low in efficiency, so is there any quick post method?

I appreciate your kind help, is means a lot especially for a newbie to MD.

Regards,

Devin

[ctan]

Hi Devin,

 

I tried your commands on some of my trajectories and found them working well. I also usually use these commands for my analysis. Not very sure what happened in your case. For VMD usage, I highly recommend you to ask to the VMD mailing list, since our answers here are not as authoritative as what you can get from VMD developers.

 

If the problem is not due to PBC, one thing you can check is the log file, where you can find the energies for each interaction term. Specifically, you can track the change of the HPS energy. If its absolute value decreased to some very small ones (~zero), then there must be some dissociation. If it just fluctuated around some non-zero value, then we can say the condensate was well maintained.

 

Hope this can help you. Please let me know if you have further questions.

 

Best,

Cheng

[fdd20]

Dear Dr. Cheng,

Thanks for your reply. I will check the log file to confirm where is wrong. In my last question, what I would like to enquire about is not VMD usage, and is about the post software you use to generate the beautiful image in the last of the tutorial.

And I will update the thread after I check the log. Thank you.

 

Best,

Devin

[fdd20]

Hi，

Dr. Cheng, I just checked the log, and it shows the HPS energy finally fluctuates about -4500. According to your reply, it is not a problem of the model, so I share the dcd and log file with you. Could you please check the results to help me out? I’d appreciate  it if you could help me dig the answer.

Best,

Devin

[ctan]

Hi Devin,

 

I have checked your trajectory and found everything okay. Here is an image of the last frame from your trajectory: https://drive.google.com/file/d/1aF60WUYxnwQYjdt5VEAOAqE35lmAIG0w/view?usp=sharing

 

The VMD tcl commands I used to wrap particles is almost the same as yours:

pbc set {180.0 180.0 1800} -all -molid top
pbc box_draw -style lines -width 1 -center origin
pbc wrap -all -compound chain -center origin

 

As for the last figure in the tutorial, there is nothing special. It’s also made with VMD. You can utilize the tcl scripting language to iteratively select atoms and assign colors to them. Actually that’s exactly what I did.

 

Best,

Cheng

[fdd20]

Dear Dr. Cheng,

Thanks for your help, and the image you uploaded is the same as the one in the tutorial. I really appreciate your support and detailed instructions,  and I will check the results today.

 

 

Best regard,

Devin