[gmx-users] Positive energy .

sujithkakkat . sujithks58 at gmail.com
Wed May 14 06:39:58 CEST 2014


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.

Regards,

Sujith



On Tue, May 13, 2014 at 9:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/13/14, 11:21 AM, Rasoul Nasiri wrote:
>
>> Why do you think positive values are doubtful?
>> What matters are energy differences between different snapshots
>> The absolute energy is meaningless in the FF framework.
>>
>>
> Not entirely true.  While the actual value itself is totally force
> field-dependent and is not a free energy, the fact that the OP is getting
> positive energies in the condensed phase is strange.  It means that the
> system is net-repulsive, which should not be the case, especially if it is
> solvated in water, in which hydrogen bonding should dominate.
>
> Without more details about system size, .mdp settings, and force field
> details, it's hard to provide the OP with any real suggestions.
>
> -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
>
> ==================================================
>
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