question about namd3 performance

From: 일반대학원 생명과학부 (
Date: Fri Jul 22 2022 - 02:55:45 CDT

I try to use namd3 for absolute free energy calculation.
Input file was generated with BFEE(binding free energy estimator) (;!!DZ3fjg!7pdO97jdHguDecdjsqmEyjmBwCvw9uDp-HUAXZDs6O-jdE3IzoKjF5nPIkzA4evArQlveRjWFZcvS6l15wY$ )
Calculations include steps for bound/unbound state with restraint,
bound/unbound state with decoupling(total 4 steps)
MD simulation is done with collective variable(euler theta, phi, psi,
RMSD... restraints) and alchemy parameter on, runFEP 1.0 0.0 -0.02 in namd
config file.
For normal MD simulation which is not above case, it seems to be fast (gpu
usage >80%)
But, free energy calculations for above steps are slow (gpu usage 15%).
(for system with atom number 120,000(protein with 510 residues, solvated),
it takes more than 1 week for each steps)
Also, with using 2 gpus for single calculation, there was no enhancement in
Is it normal for this slow speed?

Server information is as follows:
           20.04.1-Ubuntu, x86_64
           Intel(R) Xeon(R) Gold 6226R CPU @ 2.90GHz
          32 processors
           NVIDIA RTX A5000 * 4EA

namd3 command is as follows:
           export CUDA_VISIBLE_DEVICES=3
           namd3 +p8 001.1_fep_backward.conf > 001.1_fep_backward.log &

Input namd config file for step(001.1_fep_backward.conf)(bound with
decoupling) is as follows:

coordinates ../complex.pdb
structure ../complex.psf
paraTypeCharmm on
parameters ../par_all36_carb.prm
parameters ../par_all36_cgenff.prm
parameters ../par_all36_lipid.prm
parameters ../par_all36_na.prm
parameters ../par_all36m_prot.prm
parameters ../toppar_water_ions.prm
parameters ../m0p.prm
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 14.0
bincoordinates ../000_eq/output/eq.coor
binvelocities ../000_eq/output/eq.vel
ExtendedSystem ../000_eq/output/eq.xsc
binaryoutput yes
binaryrestart yes
outputname output/fep_backward
dcdUnitCell yes
outputenergies 5000
outputtiming 5000
outputpressure 5000
restartfreq 5000
XSTFreq 5000
dcdFreq 5000
hgroupcutoff 2.8
wrapAll off
wrapWater on
langevin on
langevinDamping 1
langevinTemp 300.0
langevinHydrogen no
langevinpiston on
langevinpistontarget 1.01325
langevinpistonperiod 200
langevinpistondecay 100
langevinpistontemp 300.0
usegrouppressure yes
PME yes
PMETolerance 10e-6
PMEInterpOrder 4
PMEGridSpacing 1.0
timestep 2.0
fullelectfrequency 2
nonbondedfreq 1
rigidbonds all
rigidtolerance 0.00001
rigiditerations 400
stepspercycle 10
splitpatch hydrogen
margin 2
useflexiblecell no
useConstantRatio no
colvars on
source ../fep.tcl
alch on
alchType FEP
alchFile ../fep.pdb
alchCol B
alchOutFile output/fep_backward.fepout
alchOutFreq 50
alchVdwLambdaEnd 0.7
alchElecLambdaStart 0.5
alchEquilSteps 100000
runFEP 1.0 0.0 -0.02 500000

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