[gmx-users] solvation free energy, electrostatic transformation

[Justin Lemkul]

On 7/27/15 10:20 AM, Hannes Loeffler wrote:
> What happens when you do both transformations simultaneously, i.e.
> sc-coul=yes?
>

That's not a simultaneous transformation of Coulomb terms, rather sc-coul 
applies a soft-core to the Coulomb interactions.  Actually turning off vdW and 
Coulomb simultaneously is usually unstable.

-Justin

>
> On Mon, 27 Jul 2015 15:55:04 +0200
> Daniele Veclani <danieleveclani at gmail.com> wrote:
>
>> I'm trying to calculate the  solvation free energy of a molecule (M).
>>
>> I have done a VdW.  transformation.
>>
>> I have done also a  electrostatic transformation. But I get an
>> incorrect value (large overestimation of DG solvation).
>>
>> I use gromacs 5.0.4 with gromos 54a7 force fields and my .mdp file
>> (for lambda 00) is:
>> integrator               = sd
>> tinit                    = 0
>> dt                       = 0.002
>> nsteps                   = 2500000
>> comm_mode                = angular
>> nstcomm                  = 100
>> nstxout                  = 500
>> nstvout                  = 500
>> nstfout                  = 0
>> nstlog                   = 500
>> nstenergy                = 500
>> nstxout-compressed       = 0
>> cutoff-scheme            = group
>> nstlist                  = 0
>> ns_type                  = simple
>> pbc                      = no
>> rlist                    = 0
>> coulombtype              = cutoff
>> rcoulomb                 = 0
>> epsilon_r                = 1
>> vdwtype                  = cutoff
>> rvdw                     = 0
>> DispCorr                  = no
>> fourierspacing           = 0.12
>> pme_order                = 6
>> ewald_rtol               = 1e-06
>> epsilon_surface          = 0
>> tcoupl                   = berendsen
>> tc_grps                  = system
>> tau_t                    = 0.1
>> ref_t                    = 300
>> Pcoupl                   = no
>> tau_p                    = 1.0
>> compressibility          = 4.5e-05
>> ref_p                    = 1.0
>> free_energy              = yes
>> init_lambda_state        = 0
>> delta_lambda             = 0
>> calc_lambda_neighbors    = 1
>> vdw_lambdas              = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
>> 1.00 1.00 1.00
>> coul_lambdas             = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> bonded_lambdas           = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>> 0.00 0.00 0.00
>> restraint_lambdas        = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>> 0.00 0.00 0.00
>> mass_lambdas             = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>> 0.00 0.00 0.00
>> temperature_lambdas      = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>> 0.00 0.00 0.00
>> sc-alpha                 = 0.5
>> sc-coul                  = no
>> sc-power                 = 1.0
>> sc-sigma                 = 0.3
>> couple-moltype           = QUI
>> couple-lambda0           = vdw-q
>>
>> couple-lambda1           = vdw
>> couple-intramol          = no
>> nstdhdl                  = 10
>> gen_vel                  = no
>> constraints              = all-bonds  ; we only have C-H bonds here
>> constraint-algorithm     = lincs
>> continuation             = no
>> lincs-order              = 12
>>
>>
>> What's wrong?
>>
>> Best regards
>> D.V.
>

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

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

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