[gmx-users] Re: gmx-users Digest, Vol 20, Issue 9

[David van der Spoel]

Dongsheng Zhang wrote:

>Dear David,
>
>I have tried it. The difference in potential energy is very large. 
>
>The commands I used are:
>mdrun -s full2.tpr -rerun full2.trr -e full2 -o full2 -x full2 -g full2
>g_energy -f full2.edr -o energy2  (choose 5-10 )
>
>mdrun -s full3.tpr -rerun full2.trr -e full3 -o full3 -x full3 -g full3
>g_energy -f full3.edr -o energy3  (choose 5-10)
>
>part of full2.mdp is:
>
>; NEIGHBORSEARCHING PARAMETERS
>nstlist                  = 5            ; nblist update frequency
>ns_type                  = grid         ; ns algorithm (simple or grid)
>pbc                      = xyz
>rlist                    = 1.1          ; nblist cut-off        
>
>
>; OPTIONS FOR ELECTROSTATICS AND VDW
>; Method for doing electrostatics: Cut-off, 
>coulombtype              = Switch
>fourierspacing           = 0.1
>pme_order                = 3
>rcoulomb                 = 1.0
>rcoulomb_switch          = 0.9
>; Dielectric constant (DC) for cut-off or DC of reaction field
>epsilon-r                = 1.0
>
>; Method for doing Van der Waals
>vdw-type                 = Switch
>; cut-off lengths       
>rvdw                     = 1.0
>rvdw_switch              = 0.9
>
>; Apply long range dispersion corrections for Energy and Pressure
>DispCorr                 = no; EnerPres
>
>
>
>; OPTIONS FOR WEAK COUPLING ALGORITHMS
>; Temperature coupling  
>Tcoupl                   = nose-hoover ;berendsen
>; Groups to couple separately
>tc-grps                  = protein SOL
>; Time constant (ps) and reference temperature (K)
>tau_t                    = 0.1   0.1
>ref_t                    = 300   300
>; Pressure coupling     
>Pcoupl                   = Parrinello-Rahman ;berendsen
>Pcoupltype               = isotropic 
>; Time constant (ps), compressibility (1/bar) and reference P (bar)
>tau_p                    = 1.5
>compressibility          = 4.5e-5
>ref_p                    = 1.0   
>
>
>
>part of full3.mdp is:
>
>; NEIGHBORSEARCHING PARAMETERS
>nstlist                  = 5            ; nblist update frequency
>ns_type                  = grid         ; ns algorithm (simple or grid)
>pbc                      = xyz
>rlist                    = 1.0          ; nblist cut-off        
>
>
>; OPTIONS FOR ELECTROSTATICS AND VDW
>; Method for doing electrostatics: Cut-off, 
>coulombtype              = Cut-off
>fourierspacing           = 0.1
>pme_order                = 3
>rcoulomb                 = 1.0
>rcoulomb_switch          = 0.9
>; Dielectric constant (DC) for cut-off or DC of reaction field
>epsilon-r                = 1.0
>
>; Method for doing Van der Waals
>vdw-type                 = cut-off
>; cut-off lengths       
>rvdw                     = 1.0
>rvdw_switch              = 0.9
>
>; Apply long range dispersion corrections for Energy and Pressure
>DispCorr                 = no; EnerPres
>
>
>
>; OPTIONS FOR WEAK COUPLING ALGORITHMS
>; Temperature coupling  
>Tcoupl                   = nose-hoover ;berendsen
>; Groups to couple separately
>tc-grps                  = protein SOL
>; Time constant (ps) and reference temperature (K)
>tau_t                    = 0.1   0.1
>ref_t                    = 300   300
>; Pressure coupling     
>Pcoupl                   = Parrinello-Rahman ;berendsen
>Pcoupltype               = isotropic 
>; Time constant (ps), compressibility (1/bar) and reference P (bar)
>tau_p                    = 1.5
>compressibility          = 4.5e-5
>ref_p                    = 1.0   
>
>
>
>I am using Gromacs 3.2.1 and amber94 FF. The water model is
>ffamber_tip3p.itp
>
>Could you please give me a clue where the difference in potential energy is from?
>  
>

Yes. When you use a cut-off interactions between neutral charge groups 
are always calculated completely. With an atomic switch function it you 
are calculating interactions between e.g. only the oxygen in a water 
molecule and some other charged moiety, this group based cut-off is 
described in the gromacs manual, the artifacts due to the switch in the 
paper I mentioned recently. Solution: use PME.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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