[gmx-users] solvation free energy, electrostatic transformation

[Daniele Veclani]

Yes I have a experimental value.

DGexp=1.99 kcal/mol
DGcalc.=-14.36 kcal/mol

But if I stop the VdW transformation, i get:
DGonlyVdW= 2.38 and this value is in line with other data found in the
literature.

Thank you for your answer

D.V.

2015-07-27 16:08 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 7/27/15 9:55 AM, Daniele Veclani 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).
>>
>>
> So presumably you have an experimental value of DGsolv?  How different are
> the values?
>
>
>  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?
>>
>>
> If you're getting a result that does not agree with a known quantity,
> without any errors in the run or the analysis, it means your topology for
> that molecule is bad and needs to be better parametrized.
>
> -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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