[gmx-users] Positive energy .
sujithkakkat .
sujithks58 at gmail.com
Thu May 15 06:45:25 CEST 2014
Hello Justin,
I looked at the energy components. What I find is that Short Range LJ is
highly positive (208522 kJ/mol) . Also the short range coulomb interaction
(-2028.46 kJ/mol) , although negative looks weak (I think so , because an
earlier minimization of a system with methane( oplsaa) in water (tip4p_Ice)
gave a more negative value for short range coulomb. I expect CO2 to have
stronger coulombic interactions with water ) .
Do you think any of the cutoff values in .mdp are really bad? I tried
changing them but still kept getting poor results.
Regards,
Sujith.
On Wed, May 14, 2014 at 8:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> ==================================================
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