LabInfo

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Welcome, Ren Lab Members!

 

General Information

Lab Website

https://biomol.bme.utexas.edu/  

Office Number

BME 3.516  

Dr. Ren's Office Number

BME 5.202M  

Communication and File Sharing

Slack

  • utren.slack.com
  • accounts will be created for new lab members/rotation students
  • noteworthy channels
      1. software for discussing various lab software + issues
      2. cat for sending cat pics
      3. paper-literature for sharing helpful papers + interesting new general papers
      4. amoebaplus
      5. poltype
      6. general - general Ren lab stuff
      7. allinclude - basically general but including some Schnieders lab members

Lab Meetings

https://docs.google.com/spreadsheets/d/12CtRu4sRDFdVpoSyqjxILoOML9w5Ktnp6j1QITMnH2U/edit?usp=sharing

Individual Meetings

https://docs.google.com/spreadsheets/d/1yLw5xenlOgIdsylFVk4fDnu7s5juZvgFgU8ztYvMfQE/edit?pli=1#gid=0  

Cluster Sign-Up Sheet

https://docs.google.com/spreadsheets/d/1EOlUwFpdNU2uBZ5XrHSvZnRYCUCOw5tCSkFisTm3big/edit?pli=1#gid=0 

Suggested Literature (in Box)

https://utexas.app.box.com/folder/103794407727  

Learning and reading

You are expected to learn from your labmates and by reading literature regularly. Most learnings in grad school/postdoc training are not from classroom!

You will run MD simulations and free energy calculations, using polarizable force field AMOEBA. These are expertise our lab has developed over past two decades so anyone to graduate from this lab should understand how and why on the following relevant subjects. You all should spend time read papers and documents I have been sharing. If you don't understand what you do and only run others' scripts to get numbers, you won't go far.

  • Polarizable multipole force field AMOEBA. why and how
    • Understand AMOEBA model (read slides and latest review paper Jing et al)
    • Using POLTYPE to get parameters and understand what POLTYPE is doing (read POLTYPE papers)
  • Hydration free energy. Salt effect and charge correction (if solute has net charge)
    • FEP and BAR
    • Other methods including TI and WHAM (PMF)
  • Binding free energy calculations
    • restraint and standard state correction
    • Neutralizing counter ion and background salt; what to do when ligand has net charge
    • It is OK to use other's script (Brandon, CW) to set thing up and learn. But you need to know what the program is doing, how and why again.
  • How to compile Tinker CPU and GPU code

Many topics above found on lab wiki (https://biomol.bme.utexas.edu/tinkergpu) and a BOX folder I shared with lab members (for example AMOEBA folder has slides and papers introducing AMOEBA). If you don't have/see anything or have question, contact asap. It is important to establish a routine, setting aside time to read regularly (daily, weekly). I would start from basic and whatever relevant to what you are doing now and gradually cover more and more.

Lab Resources

Disk spaces

Your home dir is in /home/YOURUSERNAME, which is physically on Nova and space is limited. But each of you have space in /work/YOURUSERNAME (physically on SUN), which is at least 2 TB (more if needed). You can access home and work dir similarly on all computers in the lab. If you have MD jobs producing large trajectories and you wan to keep them for analysis (until paper pub), please use /work. You can check your space and quota limits in /opt/quota.* Once you reach quota you can not log in or execute commands.

Use lab cluster

https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Tinkergpu:Newuser

Cluster Monitoring

https://biomol.bme.utexas.edu/ganglia/?c=NOVA&m=load_one&r=hour&s=by%2520name&hc=4    

GPU Monitoring

https://biomol.bme.utexas.edu/~rq875/checkgpu.log  

Tinker Tutorials

https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Tinkergpu:Tinker-tut    

Poltype Github

https://pren.github.io/poltype/    

Linux Utilities

https://docs.google.com/document/d/1cnmSItdRXDBcpVBGhwDahJVJ2jeh4l2oDVpMBLtlySE/edit  

Lab Guide for Grad Students

https://docs.google.com/document/d/1PKyWNTntusPeRrOiGaLAkUvJbuuc4cVBfE4Lo9ZMt2I/edit    

UT Resources

Ombuds

Employee Assistance Program

Counseling

Wellness (sometimes has fitness videos)

Night rides (Lyft discount)

University Health Services

COVID testing

Women’s Health

Free nurse advice line

Student Emergency Services

Services offered https://deanofstudents.utexas.edu/emergency/howwecanhelp.php 

Student Emergency Fund

Services for Students with Disabilities

Life in Austin

Coffee Shops

Food

Essential Stores

 

Outdoor Landmarks / Hiking

Highest point in Austin, not much of an actual hike

Pennybacker Bridge (park on side of road, can go up either side of road)

Overlook Trail (3ish miles each way, nice overlook part way, decent elevation change)

Bat Observation

  • https://goo.gl/maps/ZHfnn54qKY6icEq3A
  • Austin has a bat colony. The bats migrate but they like to hang out under the Congress bridge.
  • You can park in a paid lot or take the bus and watch the bats fly sometime around sunset. You can also watch the bats from the river or on top of the bridge.
  • It’s really neat and an Austin staple. Sometimes there are a lot of people.

Parks to wander around near campus

Pet Care Resources

  • Sometimes you can get pet supplies at the APA thrift stores
  • Austin is very dog friendly and has many dog parks

Great web resources