FAQ
Frequently Asked Questions (FAQ) about attending GaMD Workshop 2024
Q: How to connect to GaMD workshop server for running simulations if you have requested 黑料网 computing support?
A: You can find detailed instructions at /pharm/miaolab/wp-content/uploads/sites/1385/2024/10/Intruction-to-connect-GaMD-workshop-server.pdf.
Q: Which software tools are required for attending the GaMD workshop?
A: Participants will need PyMOL or VMD to visualize simulation structures. For plotting 2D free energy profiles, software tools such as OriginPro, MATLAB, or similar alternatives can be used. Additionally, SSH clients like PuTTY and MobaXterm are required to upload and download files through the 黑料网 cloud server.
Q: “pmemd.cuda: command not found” error, what should I do?
A: Ensure that the AMBER environment is properly configured using the source command:
source /shared/apps/software/amber24/amber.sh ## this needs to be updated according to your own local system
Q: How to fix limitation of the maximum number of TI atoms for running PPI-GaMD simulations?
A: To address the limitation on the maximum number of TI atoms, adjust the MaxNumberTIAtom parameter in the ${AMBERHOME}/src/pmemd/src/gti_controlVariable.i file. Increase MaxNumberTIAtom to a value that exceeds the maximum number of TI atoms specified in TIMASK1 and SCMASK1, according to your system’s requirements. After making these adjustments, recompile the AMBER24 code with the updated gti_controlVariable.i file.
Q: How do I resolve issues in PyReweighting calculations?
A: The PyReweighting toolkit is available for the Python2 and Python3 versions (/pharm/miaolab/resources/pyreweighting/). Make sure that you’re using the correct version of the scripts. Additionally, PyReweighting depends on the numpy and scipy libraries; make sure that these libraries are correctly installed and functioning. Lastly, the number of data points in the reaction coordinate file(s) need to match that of boost potential weights for reweighting. If they are inconsistent, you may encounter the errors like “ValueError: the number of columns changed from 3 to 2 at row yyy”.
Q: Where can I download the tutorial files?
A: You can download the tutorial with the required simulation and analysis files in compressed tar.bz2 files at:
GaMD tutorial:听(24.5惭叠)
LiGaMD3 tutorial: (33.7MB)
PPI-GaMD tutorial: (16MB)
PyReweighting: (12KB)