@@rohanpai5024 no you don't need to change anything in the file. However, you may need to divide the total time into smaller steps due to the time limit of the gpu on colab
@@computational_biophysics Thank You, I mean to say that when i ran a 1 ns i got only 10 frames in dcd file, so how do i increase this output frames and thus if i keep 10 ns how to adjust number of frames in output etc. sorry for the trouble
@@rohanpai5024 if you want to increase the number of frames produced each nano you can change the number of dcdfreq option (decrease it). you can find it at the start of the file
Do you have any idea why I'm getting the error "FATAL ERROR: CUDA error cudaCreateTextureObject(&gridTexObj, &resDesc, &texDesc, NULL) in file src/CudaPmeSolverUtil.C, function setupGridTexture, line 586" after starting the simulation ? I tried +idlepoll +setcpuaffinity to the command as well bu still the same error, any ideas ? thanks :)
This is very helpful. Thank you.
Would you be having all the scripts in one place, in a document?
The commands you need are in the notebook provided in the description
Thank You for the prompt response. Also what if I change the time to 10 ns in production file. Do i have to change any other values as well ?
@@rohanpai5024 no you don't need to change anything in the file. However, you may need to divide the total time into smaller steps due to the time limit of the gpu on colab
@@computational_biophysics Thank You, I mean to say that when i ran a 1 ns i got only 10 frames in dcd file, so how do i increase this output frames and thus if i keep 10 ns how to adjust number of frames in output etc. sorry for the trouble
@@rohanpai5024 if you want to increase the number of frames produced each nano you can change the number of dcdfreq option (decrease it). you can find it at the start of the file
Do you have any idea why I'm getting the error
"FATAL ERROR: CUDA error cudaCreateTextureObject(&gridTexObj, &resDesc, &texDesc, NULL) in file src/CudaPmeSolverUtil.C, function setupGridTexture, line 586" after starting the simulation ? I tried +idlepoll +setcpuaffinity to the command as well bu still the same error, any ideas ? thanks :)
Sorry I don't know how to solve this error but I think colab developers can help you.
Is it possible to edit and save the configuration file directly on google colab?
Yes. Just change the extension of the configuration file from .inp to .txt then double click the file and it will open in colab
Thank for sharing this
You are welcome
السلام عليكم
بعد production step لم اتحصل على DCD file
و عليكم السلام
هل اتاكدت انه اشتغل ال production step ؟
و بالنسبة لل equilibration هل طلع dcd ؟
@@computational_biophysics no dcd file , just the log file of output
@@computational_biophysics no dcd file from equilibration step and production
Can u please show how to do MD in gromacs and colab
i will record a video and upload it soon
You can watch how to download GROMACS and how to use it here
ua-cam.com/video/Uo41OLz1gBE/v-deo.html