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 <jalem...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? 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