[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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