HaCTang's Group

Background

Connecting modern IDEs like Cursor to HPC compute nodes can be highly frustrating. Many SLURM clusters enforce strict security policies: they block inbound internet access, disable outbound internet on compute nodes (breaking tools like Ngrok or Pinggy), and restrict standard SSH access via GSSAPI (Kerberos) or PAM, effectively disabling standard SSH key authentication.

To bypass these restrictions without root privileges, we can run a User-Space SSH Daemon (SSHD) directly on the compute node. By binding it to a high port (e.g., 22222) and running it under your own user account, it bypasses system-level Kerberos/PAM restrictions and allows seamless connections via your local SSH keys.

One of the most powerful tools of Cursor is codespace indexing. However, on remote servers, this function is prone to fail due to network limitations or fire walls. The functionality of Cursor has been greatly compromised. We can enable remote hosts to access external websites through the network interface of their own computers.

Accurate structure prediction of biomolecular complexes is crucial for understanding biological processes and enabling drug discovery. While AlphaFold3 represents a significant advancement, enhancing its accuracy for specific binding sites remains a challenge. We present SiteAF3, a novel method for accurate site-specific folding via conditional diffusion, built upon the AlphaFold3 framework. SiteAF3 refines the diffusion process by fixing the receptor structure and optionally incorporating binding pocket and hotspot residue information. Comprehensive evaluations on protein-small molecule, protein-peptide, and protein-nucleic acid datasets demonstrate that SiteAF3 consistently outperforms AlphaFold3, achieving higher accuracy in complex structure prediction especially for orphan proteins and allosteric ligands, with reduced computational cost. SiteAF3 offers a user-friendly plug-in compatible with AlphaFold3, providing a valuable tool for more accurate modeling of biomolecular interactions..

Found the installation path of Cursor on your own PC (rather than server).

Found product.json in cursor\resources\app

Change all marketplace.cursorapi.com into marketplace.visualstudioapi.com

Installation

After login, use nano or vim to modify ~/.bashrc. Add the following code to the end of ~/.bashrcand save the file:

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export PATH="/opt/Gromacs2024/install/bin:$PATH"
alias gmx24='/opt/Gromacs2024/install/bin/gmx_mpi'

Here I rename the command gmx_mpi as gmx24 to avoid command conflict when using Gmx18 on the same machine.

Then in shell:

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source ~/.bashrc

Test if Gmx24 is initialized successfully：

Installation

After login, use nano or vim to modify ~/.bashrc. Add the following code to the end of ~/.bashrcand save the file:

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. /opt/miniconda/etc/profile.d/conda.sh
export PATH="/opt/miniconda/bin:$PATH"

蕞蕞蕞白痴的用法

以Github为例（默认已经安装了Gitbash）：

首先创建一个repo，

Science and Practice Training一书中写道力量训练所应该包括的模块分别是：dynamic动态，即极限速度训练；maximum极大值，即极限重量训练；repetition重复，即辅助训练。

拥有一个强大的脊柱，意味着脊柱在冠状面和矢状面以及旋转时都拥有非凡的灵活度和稳定性。通过针对性训练可以逐步增强我们的脊柱，改善体态，提高运动表现。