From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Feb 05 2014 - 15:10:53 CST
if your system isn't solvated, and your just doing that molecule on its
own, you don't need PME or periodic conditions. In fact, in this case your
cutoff is larger than the periodic dimensions, which is a bit odd in most
cases. So unless this is really what you want, I would remove all of the
PME and periodic stuff.
On Wed, Feb 5, 2014 at 1:44 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
> 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
>
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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