[gmx-users] .mdp file for Enthalpy of Vaporization calculation

[Justin Lemkul]

On 4/4/17 6:21 AM, Matteo Busato wrote:
> Goodmorning to everyone,
>
>
> I'm writing here because I'm trying to perform a calculation about the Enthalpy of Vaporization of a system with 434 molecules of an ionic liquid. I've already read all the previous posts in the forum about this subject and it has come clear to me how to perform the calculation, however I'm having problems with my .mdp file when trying to perform the NVT equilibration.
>
> I've read that for such calculation cutoffs must be set = 0 and pbc=none, however with such parameters I'm forced to use cutoff-scheme=group instead of Verlet, so the first problem is that 'group' is not configured for GPU acceleration and I can use just 1 MPI rank (which slows the job time a lot). Is there a way to perform this calculation with Verlet?
>
> The second problem is that if I set rvdw=0, gromacs gives me an error saying that (obviously), vdw-switch must be < rvdw. How can I solve this issue?
>

There's nothing to switch; you're using a plain cutoff.

There's no point trying to use a GPU to simulate one molecule.  This simulation 
should run in a matter of seconds on a single CPU.

-Justin

> I'll post the mdp I'm using here. Thank you in advance.
>
>
> ; Run control
> integrator               = sd       ; Langevin dynamics
> tinit                    = 0
> dt                       = 0.001
> nsteps                   = 1000000    ; 1000 ps
> nstcomm                  = 100
> ; Output control
> nstxout                  = 500
> nstvout                  = 500
> nstfout                  = 0
> nstlog                   = 500
> nstenergy                = 500
> nstxout-compressed       = 0
> ; Neighborsearching and short-range nonbonded interactions
> cutoff-scheme            = group
> nstlist                  = 0
> ns_type                  = grid
> pbc                      = no
> rlist                    = 0
> ; Electrostatics
> coulombtype              = cutoff
> rcoulomb                 = 0
> ; van der Waals
> vdwtype                  = cutoff
> vdw-modifier             = potential-switch
> rvdw                     = 0
> rvdw-switch              =0
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order                = 6
> ewald_rtol               = 1e-06
> epsilon_surface          = 0
> ; Temperature coupling
> ; tcoupl is implicitly handled by the sd integrator
> tc_grps                  = system
> tau_t                    = 1.0
> ref_t                    = 298.15
> ; Pressure coupling is off for NVT
> Pcoupl                   = No
> tau_p                    = 0.5
> compressibility          = 4.5e-05
> ref_p                    = 1.0
> ; Generate velocities to start
> gen_vel                  = yes
> gen_temp                 = 300
> gen_seed                 = -1
> ; options for bonds
> constraints              = h-bonds  ; we only have C-H bonds here
> ; Type of constraint algorithm
> constraint-algorithm     = lincs
> ; Do not constrain the starting configuration
> continuation             = no
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order              = 12
> dispcorr=no
>
>
> Matteo Busato
>

-- 
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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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