Native Amber Support for GPU Constant PH Implicit Solvent

[Gregory Schwing]

Dear AMBER developers:

I am interested in clarifying what exactly is happening when I follow the constant PH tutorial and use pmemd.cuda.  My two questions are following:


  1.
 What is the difference between the two manners of passing in parameters for running constant PH simulations?

There is method 1 (Constant PH tutorial approach https://ambermd.org/tutorials/advanced/tutorial18/)
TLEAP
"source leaprc.constph"
command line (e.g., AS4/GL4 dihedrals)
cpinutil.py -resnames HIP GL4 AS4 -p protein.prmtop -o protein.cpin
pmemd.cuda [...] -cpin cpin_file.in -cpout protein.prod.cpout -cprestrt protein.prod.cprestrt

Method 2 (GBNECK Patch Shen Lab Approach https://gitlab.com/shenlab-amber-cphmd<https://gitlab.com/shenlab-amber-cphmd>)
TLEAP
# Load the ff14SB force field
source leaprc.protein.ff14SB

# Set PBradii to mbondi3 (required for GBNeck2 in CpHMD)
set default PBradii mbondi3

# Load the CpHMD residue definitions (AS2 and GL2)
loadoff phmd.lib

# Load force field modifications for CpHMD (e.g., AS2/GL2 dihedrals)
loadamberparams frcmod.phmd

pmemd.cuda [...] -cpout protein.prod.cpout -cprestrt protein.prod.cprestrt \
-phmdparm gbneck2_input.parm -phmdin ph.mdin -phmdout protein.prod.lam -phmdrestrt protein.prod.phmdrst



  1.
How much of the calculation is on the GPU?  Are implicit solvent constant PH simulations accurate when using pmemd.cuda?

Continuous constant pH MD can be performed in three modes: implicit solvent (iphmd=1, only available in
CPU),[676–678] hybrid solvent (iphmd=2),[679] and all-atom (iphmd=3). [680–682] In the implicit-solvent mode,
both conformational and protonation state sampling is performed using a generalized Born (GB) model. [...] The implicit-solvent mode makes uses of the GBNeck2 model[28], and it is implemented for both CPUs[677] and GPUs[678], although the GPU version is currently only available through a downloadable patch (https://gitlab.com/shenlab-amber-cphmd/cphmd-patches). By contrast, the all-atom mode (iphmd=3) is implemented only for GPUs.[682]

Thank you in advance for your time,
Greg
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