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 ." <sujithk...@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 <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? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
