Re: About CUDA version of NAMD 2.7 B1

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Mar 25 2009 - 08:34:29 CDT

The CUDA code in NAMD 2.7b1 is an undocumented, incomplete, experimental
feature that is not suitable for production use. Wait for 2.7b2.

-Jim

On Wed, 25 Mar 2009, wang wrote:

> Dear all ,
> I succeed to compile the cuda version of NAMD 2.7 b1.
> When I ran a case, the program stopped in the minimize step 553.
> And there is any error message occurred .
> Could you tell me how to fix the problem ?
> Thank you .
>
> Y. T Wang
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> input file
> ----------------------------------------------------------------------------------------------------------------------------------------
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
> structure cg27wang.psf
> coordinates cg27wang.pdb
> set temperature 310
> set outputname cg
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters rbcg-2007.par
> temperature $temperature
> # Force-Field Parameters
> exclude 1-2
> cutoff 12.0
> switching on
> switchdist 9.0
> pairlistdist 16.0
> hgroupcutoff 0
> # Integrator Parameters
> timestep 5.0
> nonbondedFreq 1
> stepspercycle 20
> # Constant Temperature Control
> langevin off
> langevinPiston off
> # Periodic Boundary Conditions
> cellBasisVector1 150.0 0. 0.
> cellBasisVector2 0. 150.0 0.
> cellBasisVector3 0. 0 150.0
> cellOrigin 0.0 0.0 0.0
> wrapAll on
> margin 6.0
> dielectric 20
> # Output
> outputName $outputname
> restartfreq 10
> dcdfreq 1000
> xstFreq 1000
> outputEnergies 100
> outputPressure 100
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
> # Minimization
> minimize 1000
> reinitvels $temperature
> run 20000000
>
>
> output
> ---------------------------------------------------------------------------------------------------------------------------------------------
> PRESSURE: 553 4.1798e+06 -231322 120605 -231322 4.15516e+06 -222828
> 120605 -222828 4.16118e+06
> GPRESSURE: 553 4.1798e+06 -231322 120605 -231322 4.15516e+06 -222828
> 120605 -222828 4.16118e+06
> ENERGY: 553 235.3469 746.7691 1723.1719 0.0000 0.0000 47938516.6039
> 0.0000 0.0000 0.0000
> 47941221.8918 0.0000 47941221.8918 47941221.8918 0.0000 4165380.2214
> 4165380.2214 3375000.0000 4165380.2214 4165380.2214
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