Yinglong Miao

HI Alessandro, We normally take the PMF data and use Origin Pro to plot the 2D free energy profiles. With that, you can easily adjust the energy contour lines For python, you may need to look up more to find the options. Best, Yinglong

In this case, it should be ok. Yinglong

The membrane might be OK. Were you able to finish all the GaMD equilibration steps, or did the program crash/exit earlier? Yinglong

It should be "accelMDGRestartFile" as described in the NAMD documentation and GaMD-NAMD manual: https://www.med.unc.edu/pharm/miaolab/resources/gamd/manual-namd/. It was a typo on the GaMD-NAMD tutorial webpage (in the first place): https://www.med.unc.edu/pharm/miaolab/resources/gamd/tutorial-of-gamd-in-namd/; just corrected. I don't remember exactly, but you may find the two lines you need in the NAMD log file for the gamd-restart.dat file. Yinglong

Sounds good! Yinglong

Hi Gideon, I was wondering how many steps did you put for the "run" command. The number of steps there should be at least the sum of "accelMDGcMDSteps" and "25000000". You can look at example input settings at: https://www.med.unc.edu/pharm/miaolab/resources/gamd/tutorial-of-gamd-in-namd/ Hope this helps, Yinglong

Hi Gideon, Your simulation config file looks ok to me. As for the system density / size change, could you possibly run longer cMD NPT equilibration and then use the “equilibrated” system restart files to continue with GaMD simulation? You can also test “increase margin, or disable useFlexibleCell for liquid simulation” as suggested in the output. Best, Yinglong Yinglong Miao, Ph.D. Associate Professor Computational Medicine Program and Department of Pharmacology University of North Carolina - Chapel...

Hi, The GaMD parameter settings should be similar for membrane proteins as for globular proteins. One one note for your “accelMDGStatWindow”, you may need to set it to a smaller number: accelMDGStatWindow < No. of steps to calculate average and standard deviation in GaMD > Acceptable Values: Integer Default Value: -1 Description: The number of simulation steps used to calculate the average and standard deviation of potential energies, as well as the frequency of recalculating the boost potential...