From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Wed Feb 05 2014 - 12:44:35 CST
Hi Rawan,
Your system is tiny - just 2.7 Angstroms along “x” and “z” and 5 Angstroms along “y”. You should have at least 5 PME grid points along each direction, otherwise NAMD throws that error. If your system sizes are correct, try setting pmeGridSpacing to 0.5.
Maxim
On Feb 5, 2014, at 12:28 PM, Bennion, Brian <Bennion1_at_llnl.gov> wrote:
> maybe no pme grid sizes are given in your conf file?
> It is turned on but no dimensions are given for x y or z axes.
>
> Brian
>
> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Rawan Al Nsour [alnsourra_at_vcu.edu]
> Sent: Wednesday, February 05, 2014 10:00 AM
> To: namd-l
> Subject: namd-l: PMEGridSizeX (number of grid points) is very small.
>
> Dear All,
> I ran a simulation for small molecular C4F10 and it is failed, what is the solution in this case?
> below is the conf file
> structure ptfe.psf
> coordinates ptfe.pdb
> outputName nvt-01
> set temperature 280
> firsttimestep 0
> paraTypeCharmm on
> parameters par_all27_prot_lipid.inp
> temperature $temperature
> # Periodic Boundary Conditions
> # NOTE: Do not set the periodic cell basis if you have also
> # specified an .xsc restart file!
> if {1} {
> cellBasisVector1 2.7 0.0 0.0
> cellBasisVector2 0.0 5.06 0.0
> cellBasisVector3 0.0 0.0 2.7
> cellOrigin 0.0 0.0 0.0
> }
> wrapAll on
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 7.0
> switching on
> switchdist 5.0
> pairlistdist 8.5
>
> # Integrator Parameters
> timestep 0.5 ;# 1fs/step
> rigidBonds none ;# needed for 1fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
>
> #PME (for full-system periodic electrostatics)
> if {1} {
> PME yes
> PMEGridSpacing 1.0
> }
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
>
> restartfreq 50 ;# 500steps = every 1ps
> dcdfreq 25
> xstFreq 25
> outputEnergies 10
> outputPressure 10
> minimize 50
> run 250 ;# 0.1 ns
>
> Thanks,
> --
> Rawan Al Nsour
> Ph.D. Candidate
> Department of Mechanical and Nuclear Engineering
> School of Engineering, Virginia Commonwealth University
> E-mail: alnsourra_at_vcu.edu
> 401 W. Main Street, Room E3216
> P.O. Box 843015
> Richmond, Virginia 23284-3015
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