[gmx-users] Semiisotropic pressure coupling

[Justin Lemkul]

On 2/13/15 11:55 AM, shivangi nangia wrote:
> Dear Justin,
>
> Thanks again for the reply.
>
> I used cutoff scheme=group and vdwtype=shift, but I still get the error,
> even though I have not specified any vdw-modifier anywhere in the md file:
>
>   Invalid enum 'force-switch' for variable vdw-modifier, using
>    'Potential-shift-Verlet'
>    Next time use one of: 'Potential-shift-Verlet' 'Potential-shift' 'None'
>    'Potential-switch' 'Exact-cutoff'
>

With the group scheme, there should be no vdw-modifier read.  Something is wrong 
with your input file.

>
> .mdp now is: (non bonded interactions in bold)
>
> ; RUN CONTROL PARAMETERS
>
> dt                       = 0.002
> nsTEPS                   = 25000000 ;50ns
>
> integrator             = md
> ld-seed                 = -1
>
> ; mode for center of mass motion removal
> comm-mode                = Linear
> ; number of steps for center of mass motion removal
> nstcomm                  = 10
>
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout                  = 50000
> nstvout                  = 50000
> energygrps               = Protein     Non-Protein
> ; Output frequency for energies to log file and energy file
> nstlog                   = 100
> nstcalcenergy            = -1
> nstenergy                = 100
>
> nstxtcout                = 500
> xtc-precision            = 1000
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist                  = 1
> ; ns algorithm (simple or grid)
> ns-type                  = Grid
> ; Periodic boundary conditions: xyz, no, xy
> pbc                      = xyz
> periodic_molecules       = no
> ; nblist cut-off
> rlist                    = 1.2
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype              = PME
> ;rcoulomb-switch          = 0
> rcoulomb                 = 1.2
> fourierspacing           = 0.16
> pme_order                = 4
> optimize-fft            = yes
> ;* Method for doing Van der Waals*
>
> *vdw-type                 = shift*
> *; cut-off lengths*
> *rvdw-switch              = 1.0*
> *rvdw                     = 1.2*
>
> *cutoff-scheme = group*
> *DispCorr = no*
> ; OPTIONS FOR BONDS
> constraints              = none
> ; Type of constraint algorithm
> constraint-algorithm     = Lincs
> lincs-order             = 6
>
>
> ; temperature controls
> tcoupl                  = v-rescale
> tc-grps                 = Protein       Non-Protein
> tau-t                   = 1.0   1.0
> ref-t                   = 303    303
>
> ; Pressure Controls
> pcoupl                  = Parrinello-Rahman
> pcoupltype              = semiisotropic
> tau-p                   = 1.0
> ref-p                   = 1.0 1.0
> compressibility         = 4.5e-5 4.5e-5
>
>

This shouldn't trigger Verlet or vdw-modifier.  I don't know how you could have 
gotten the above error with this input file; likely you've mixed something up. 
Also note that you will need rlist >= 1.4 when using vdwtype = shift for proper 
energy conservation.

Or, you know, upgrade to 5.0.4 where this is all easy :)

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================