[gmx-users] Positive energy .
Mark Abraham
mark.j.abraham at gmail.com
Thu May 15 09:53:06 CEST 2014
Rather, find out what non-bonded scheme your models were parametrized to
use, and use that! These are often not free parameters!
Mark
On May 15, 2014 6:47 AM, "sujithkakkat ." <sujithks58 at gmail.com> wrote:
> 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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