Re: NAMD2.6 - 1D Periodic Boundary and PME - FATAL ERROR: PME requires periodic boundary conditions.

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Thu May 21 2009 - 15:55:42 CDT

Hi Greg,

PME requires periodic boundaries in all three dimensions.
For periodicity in just one dimension, you have to make the
"nonperiodic" dimensions longer (i.e. double the length) to
prevent the periodic images from interacting with each other.

Best regards,
Dave

On Thu, May 21, 2009 at 04:32:47PM -0400, Greg Guthe wrote:
> Hi,
>
> Does PME require periodic boundaries for all three dimensions? I'd
> like a periodic boundary and PME for just one, but NAMD throws "PME
> requires periodic boundary conditions." Is the only solution to make a
> wide periodic box or am I implementing something wrong?
>
> Thanks,
> Greg
>
> Related: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7876.html
>
> I'm using this config file:
>
> # Input Parameters
> amber yes
> ambercoor doesitexplode.rst7
> parmfile doesitexplode.parm7
>
> # Output Parameters
> outputname ./doesitexplode
> binaryoutput yes
> restartfreq 1000
> DCDfreq 100
>
> # Timestep Parameters
> numsteps 10000
>
> timestep 1.0 # (fs)
>
> # Simulation Space Partitioning Parameters
> cutoff 12
> switching on
> switchdist 10
> pairlistdist 14.5
> splitpatch hydrogen
>
> # Basic Dynamics Parameters
> exclude none
> temperature 300 # (K) room temp 20C
>
> # Periodic Box Boundaries
> cellBasisVector1 0 0 25
> cellOrigin 0 0 0
> #wrapAll on
>
> # Particle Mesh Ewald (PME)
> PME yes
> PMEGridSpacing 1.0
> #PMEGridSizeZ 2
> fullElectFrequency 5
>
> # Cylindrical Harmonic Boundary Conditions
> #cylindricalBC on
> #cylindricalBCCenter 0 0 10
> #cylindricalBCr1 50
> #cylindricalBCl1 1500 # i.e. long
> #cylindricalBCk1 50
>
> # Fixed Atom Parameters
> #fixedAtoms yes
> #fixedAtomsFile fixedfixed.pdb
>
> # Langevin Dynamics Parameters
> #langevin yes
> #langevintemp 300

-- 
David J. Hardy           office: 3047 BI
Beckman Institute        fax:    (217) 244-6078
University of Illinois   phone:  (217) 244-5493
405 N. Mathews Ave       email:  dhardy_at_ks.uiuc.edu
Urbana, IL 61801, USA    web:    http://www.ks.uiuc.edu/~dhardy/

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