[gmx-users] Semiisotropic pressure coupling

[shivangi nangia]

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'


.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




***************************************************************************************************************************8


On Fri, Feb 13, 2015 at 9:39 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/12/15 10:34 PM, shivangi nangia wrote:
>
>>
>>> Dear Justin,
>>>
>>>
>> Thanks for the reply.
>>
>> The link you have mentioned says the parameters are for GROMACS 5.0
>>
>> I am using an older version, 4.6.1
>>
>> Is there another link/suggestions for that version.
>>
>> Sorry, I forgot to mention.
>>
>> On trying to use those parameters with my version of GROMACS, I get the
>> error:
>>
>> ERROR 1 [file md.mdp, line 78]:
>>    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'
>>
>>
>> The mdp options manual says:
>>
>> *Force-switch*Smoothly switches the forces to zero between *rvdw-switch*
>>   and *rvdw*. This shifts the potential shift over the whole range and
>> switches it to zero at the cut-off. Note that this is more expensive to
>> calculate than a plain cut-off and it is not required for energy
>> conservation, since *Potential-shift* conserves energy just as well
>>
>> Can I use Potential-shift instead of my version?
>>
>
> No.  Read the description of Potential-shift: "Note that this does not
> affect the forces or the sampling."  Force-switching is required for proper
> use of the lipid force field.  The old "vdwtype = shift" with the group
> cutoff scheme should do the same thing as force-switch, but we haven't
> tested it explicitly. What i know for sure is that CHARMM's vfswitch and
> GROMACS' "vdw-modifier = force-switch" produce identical forces, hence the
> strong recommendation.
>
>
> -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
>
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