Implementation of the pH exchange.

[shantenujha]

Implementation of the pH exchange.

"In pH-REMD, although the manipulation of mdin file is kind of trivial, there's actually an additional input file called cpin file which needs to be generated using a script in Amber called cpinutil.py. The procedure is not very straightforward so we shall discuss about it together some time. If you want to get an idea of it, please refer to page 440-456 in the newest Amber manual (http://ambermd.org/doc12/Amber16.pdf) or check out the Amber tutorial for const-pH MD (http://ambermd.org/tutorials/advanced/tutorial18/)"

If I understand correctly cpinutil.py utility should be only called during the input file preparation stage. In addition, command line arguments would be slightly different, due to the need to pass .cpin file.

The first question is: what is the target molecule and which set of input files should be used?

Another question is are we interested in implicit or explicit solvent at this point?

The main question is how do we populate swap matrix in pH exchange?

Srinivas: if you are interested to chip in, you can review http://ambermd.org/doc12/Amber16.pdf and http://ambermd.org/tutorials/advanced/tutorial18/ before Monday.

[shantenujha]

Antons, Vivek -- I can't seem to find a way to assign this to Srinivas. Can you help please. Thanks!

[antonst]

Done.

[antonst]

Notes from the meeting (10th February):

• Label of the exchange parameter in Amber's input file is solvph

• Energy should be obtained exactly in the same way as for salt concentration exchange

• We can prepare and use input files from the tutorial

• For now we are interested in implicit solvent

• Once we obtain energy, swap matrix is populated exactly the same as for salt concentration exchange

• There is no need to call Amber's cpinutil.py utility during the simulation.

  • for MD simulation, command line arguments are different! sander.MPI -O -i pH_<pH>.mdin -p 4LYT.parm7 -c 4LYT.equil.rst7 -cpin 4LYT.equil.cpin -o <pH>/4LYT.md1.mdout -cpout <pH>/4LYT.md1.cpout -r <pH>/4LYT.md1.rst7 -x <pH>/4LYT.md1.nc -cprestrt <pH>/4LYT.md1.cpin

[SrinivasMushnoori]

Update on pH exchange implementation:

As noted ,the exchange parameter of interest is "solvph" in the mdin file. If my understanding is correct:

First a label-value pair needs to be created in order to accept pH as an input. This would be in RepEx's input file builder, specifically _input_filebuilder.py 's lines 57-68. This has been implemented. I'm not sure if there needs to be a change made before that.

Second, there need to be cases defined where one of the exchange dimensions is pH and the umbrella dimension is one of the other dimensions. I am currently working through this.

Should I be pushing these changes to the feature/pH branch so you can look at them right now, or at a later point when I have made further changes and consolidated them?

Thanks, Srinivas