[gmx-users] Positive energy .

[Justin Lemkul]

On 5/14/14, 12:39 AM, sujithkakkat . wrote:
> Hello Justin and others,
>
>     Thank you for the response . Here are mode details of the system; ( in
> the order ; MDP settings, itp  and top files) . The system consists of 460
> water molecules and 1 CO2 molecule . I am trying to find the  free energy
> of solvation for CO2 in water at various temperatures and pressure.
>
> *MDP settings:*
>
> ; Run control
> integrator = steep
> nsteps     = 20000
>
> ; EM criteria and other stuff emtol     = 10
> emstep   = 0.01
> niter        = 20
> nbfgscorr = 10
>
> ; Output control
> nstlog       = 1
> nstenergy = 1
>
> ; Neighborsearching and short-range nonbonded interactions nstlist    = 1
> ns_type = grid
> pbc       = xyz
> rlist       = 1.0
>
> ; Electrostatics
> coulombtype = PME
> rcoulomb      = 1.0
>
> ; van der Waals
> vdw-type     = switch
>   rvdw-switch =0.8
> rvdw           = 0.9
>
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
>
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.12
>
> ; EWALD/PME/PPPM parameters
> pme_order         = 6
>   ewald_rtol          = 1e-06
> epsilon_surface  = 0
> optimize_fft        = no
>
> ; Temperature and pressure coupling are off during EM
> tcoupl  = no
>   pcoupl = no
>
> ; Generate velocities to start
> gen_vel = no
>
> ; options for bonds
> constraints = all-bonds
>
> ; 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
>
> *--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*
>
> *.itp for tip4p/Ice*
>
> [atomtypes]
> ;name     mass          charge   ptype    sigma        epsilon
> IW        0             0.000       D     0.0           0.0
> OW4       15.99940      0.000       A     0.31668       0.88211
> HW        1.00800       0.000       A     0.00000E+00   0.00000E+00
>
> [moleculetype]
> ; name nrexcl
>    water  1
>
> [atoms]
> ; nr type resnr residu atom cgnr charge      mass
> 1     OW4  1     H2O    OW1  1     0         15.994
> 2     HW   1     H2O    HW2  1     0.5897    1.008
> 3     HW   1     H2O    HW3  1     0.5897    1.008
> 4     IW   1     H2O    MW4  1    -1.1794    0.0
>
> [constraints]
> ;i j funct doh  dhh
> 1       2       1       0.09572
> 1       3       1       0.09572
> 2       3       1       0.15139
>
> [exclusions]
> 1       2       3       4
> 2       1       3       4
> 3       1       2       4
> 4       1       2       3
>
> ; The position of the dummy is computed as follows:
> ;
> ;               O
> ;
> ;               D
> ;
> ;       H               H
> ;
> ; const = distance (OD) / [ cos (angle(DOH))    * distance (OH) ]
> ;         0.015 nm      / [ cos (52.26 deg)     * 0.09572 nm    ]
>
> ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
>
> [virtual_sites3]
> ; Dummy from                    funct   a               b
> 4       1       2       3       1       0.13458         0.13458
>
>
> *---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.itp
> for CO2*
>
>
> [atomtypes]
> ; name        mass        charge     ptype    sigma    epsilon
>     D         22.0049       0.0000       A      0.0000   0.0000
>     CA         0.0000       0.6512       A      0.2757   0.2339
>     CO         0.0000      -0.3256       A      0.3033   0.6695
>
> [moleculetype]
> ; name  nrexcl
>    CO2    2
>
> [atoms]
> ; nr    type    resnr   residue    atom    cgnr   charge    mass
>    1       D       1      CO2        D1       1     0.0000    22.0049
>    2       D       1      CO2        D2       1     0.0000    22.0049
>    3      CA       1      CO2        CA       1     0.6512     0.0000
>    4      CO       1      CO2        OC1      1    -0.3256     0.0000
>    5      CO       1      CO2        OC2      1    -0.3256     0.0000
>
> [constraints]
> ; i   j   funct    doc
>    1   2     1      0.195948
>
> [virtual_sites2]
> ; i   j   k   funct   a
>    3   1   2     1     0.5
>    4   1   2     1     1.08638006
>    5   2   1     1     1.08638006
>
>
>
> *---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*
>
>
> *.top file*#include "Oplsaa.ff/forcefield.itp"
> #include "Oplsaa.ff/atomtype.itp"
> #include "Oplsaa.ff/tip4p_Ice.itp"
> #include "Oplsaa.ff/co2_epm2_dummy.itp"
> [ system ]
> ; Name
> CO2 in water
>
> [ molecules ]
> ; Compound        #mols
>    CO2              1
>    SOL              460
>
>
>
>
>
> *---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*
> Thank you for your time.
>

So what does g_energy tell you about the various components of the potential 
energy?  Which ones seem out of place?

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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