From: Aravinda Munasinghe (aravinda1879_at_gmail.com)
Date: Sun Nov 29 2020 - 09:01:30 CST
you can use 4fs with HMR.
https://pubmed.ncbi.nlm.nih.gov/26574392/
Best,
Aravinda
Aravinda Munasinghe
On Mon, Nov 23, 2020 at 6:20 AM Krishna Vkm <krishnatifr_at_gmail.com> wrote:
> Dear all
> I have simulated a peptide in the explicit solvent in NAMD 2.13 and it
> took around 2.9 hr to complete 10 ns. I needed a cheaper simulation for the
> same system, so I went for implicit MD. However, in implicit MD (using
> GBIS) of the peptide, the speed is even slower where it took 3.7 hr to
> complete 10ns. During the explicit and implicit run, the cluster condition
> is the same (same number of nodes and processor and also no other jobs were
> running) so it appears that there could be something in the configuration
> file or there is something else. I am giving below the configuration file
> for implicit and explicit MD.
> I will be really thankful for any help
>
> Regards
> Krishna
>
>
> *####Configuration file for explicit MD#####*
>
> coordinates npt-prot-free.coor
> structure step3_charmm2namd.psf
> extendedSystem npt-prot-free.xsc
> velocities npt-prot-free.vel
> # forcefield
> parameters toppar/par_all36m_prot.prm
> parameters toppar/toppar_water_ions.str
> paraTypeXplor off
> paraTypeCharmm on
> exclude scaled1-4
> 1-4scaling 1.0
> # output files
> outputname nvt-prod-50ns-1
> restartname nvt-prod-50ns-1-restart
> restartfreq 1000000
> restartsave yes
> binaryoutput no
> DCDfile nvt-prod-50ns-1.dcd
> DCDfreq 1000
> outputEnergies 100
> outputMomenta 1000
> outputTiming 1000
> #approximations
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 14.0
> splitPatch hydrogen
> hgroupcutoff 2.5
> PME yes
> PMEGridSpacing 1
> #constraints
> rigidBonds all # Reqd for a 2fs timestep.
> rigidTolerance 0.00001
> rigidIterations 100
> #integrator
> numsteps 500000
> timestep 2.0 # 2 fs timestep
> stepspercycle 10
> # simulation parameters
> COMmotion no
> dielectric 1.0
> fullElectFrequency 1
> nonbondedFreq 1
> longSplitting c1
> #temp control
> langevin on
> langevinTemp 300.0
> langevinDamping 5
> langevinHydrogen on
> #script
> run 5000000
>
> *####Configuration file for implicit MD#####*
>
> structure implicit.psf
> coordinates prot-free.coor
> velocities prot-free.vel
>
> # forcefield
> parameters toppar/par_all36m_prot.prm
> paraTypeXplor off
> paraTypeCharmm on
> exclude scaled1-4
> 1-4scaling 1.0
> # output files
> outputname prod-50ns-1
> #restartname prod-50ns-1
> restartfreq 5000000
> restartsave yes
> binaryoutput no
> #DCDfile prod-50ns-1.dcd
> DCDfreq 1000
> outputEnergies 10
> outputMomenta 1000
> outputTiming 1000
> # GBIS PARAMETERS
> gbis on
> ionConcentration 0
> sasa on
> surfaceTension 0.005
> #approximations
> cutoff 16.0
> switching on
> switchdist 15.0
> pairlistdist 18.0
> splitPatch hydrogen
> hgroupcutoff 2.5
> #constraints
> rigidBonds all
> rigidTolerance 0.00001
> rigidIterations 100
> #integrator
> numsteps 500000
> timestep 2.0
> stepspercycle 10
> # simulation parameters
> #temperature 300.0
> COMmotion no
> dielectric 1.0
> fullElectFrequency 1
> nonbondedFreq 1
> longSplitting c1
> #temp control
> langevin on
> langevinTemp 300.0
> langevinDamping 5
> langevinHydrogen on
> run 5000000
>
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