[gmx-users] Calculation of Spectroscopic properties
Dear gmx-users I am trying to calculate the optical rotation of a molecule in solution. There are several examples of this in the literature where they take snapshots of molecule at intervals throughout the trajectory, calculate optical rotation, and average them to get a solvated optical rotation. I have tried using this method by my numbers don't seem to converge on any one value, for example over 6ns trajectory, using 3000 snapshots I get a calculated rotatory power of ~20 deg/cm average with a standard deviation 745 deg/cm! (calculated with atom-dipole interaction model). my molecule does have a long carbon chain which may be the problem. So would it help to pick out the most common configurations and do calculations on them perhaps? is there a feature of gromacs that will determine the most probable conformations? Also I set up an single point energy calculation of each snapshot using mdrun -rerun (but this is on the unsolvated molecule) for possible comparison of the snapshot energies, but is there a better way of getting these energies from the energy file? Thanks in advance for any responses Cody Covington -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear gmx-users I am trying to calculate the optical rotation of a molecule in solution. There are several examples of this in the literature where they take snapshots of molecule at intervals throughout the trajectory, calculate optical rotation, and average them to get a solvated optical rotation. I have tried using this method by my numbers don't seem to converge on any one value, for example over 6ns trajectory, using 3000 snapshots I get a calculated rotatory power of ~20 deg/cm average with a standard deviation 745 deg/cm! (calculated with atom-dipole interaction model). my molecule does have a long carbon chain which may be the problem. So would it help to pick out the most common configurations and do calculations on them perhaps? is there a feature of gromacs that will determine the most probable conformations? Also I set up an single point energy calculation of each snapshot using mdrun -rerun (but this is on the unsolvated molecule) for possible comparison of the snapshot energies, but is there a better way of getting these energies from the energy file? Thanks in advance for any responses Cody Covington -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] charmm36 parameters
Dear gmx-Users I have downloaded the charmm36 force field for the gromacs website and upon inspection of ffnonbonded.itp found several charges listed as 0.00 with the comment partial charge def not found for several atomtypes I am using. Are these charges not used in charmm36? Thank You in Advance Cody Covington Below is the file ffnonbonded.itp [atomtypes] section ; ; Added new and changed old atomtypes and pairtypes (OSL, OSLP, HBL and CCL) - Thomas Pigot July 2010 ; [ atomtypes ] ;name at.num masscharge ptype sigma epsilon C 6 12.011000.51A 0.356359487256 0.46024 CA 6 12.01100-0.115 A 0.355005321205 0.29288 CC 6 12.011000.62A 0.356359487256 0.29288 CD 6 12.011000.000 A 0.356359487256 0.29288 ; partial charge def not found CE1 6 12.011000.000 A 0.372395664183 0.284512 ; partial charge def not found CE2 6 12.011000.000 A 0.370613866746 0.267776 ; partial charge def not found CM 6 12.011000.000 A 0.374177461619 0.46024 ; partial charge def not found CP1 6 12.011000.02A 0.405358916754 0.08368 CP2 6 12.01100-0.18 A 0.387540942391 0.23012 CP3 6 12.011000.00A 0.387540942391 0.23012 CPA 6 12.011000.000 A 0.320723538531 0.37656 ; partial charge def not found CPB 6 12.011000.000 A 0.320723538531 0.37656 ; partial charge def not found CPH16 12.011000.19A 0.320723538531 0.2092 CPH26 12.011000.32A 0.320723538531 0.2092 CPM 6 12.011000.000 A 0.320723538531 0.37656 ; partial charge def not found CPT 6 12.01100-0.02 A 0.320723538531 0.37656 CS 6 12.011000.000 A 0.391995435982 0.46024 ; partial charge def not found CST 6 12.011000.000 A 0.278494939291 0.242672 ; partial charge def not found CT1 6 12.011000.07A 0.405358916754 0.08368 CT2 6 12.01100-0.18 A 0.387540942391 0.23012 CT3 6 12.01100-0.11 A 0.367050271874 0.33472 CY 6 12.01100-0.03 A 0.355005321205 0.29288 CT 6 12.011000.000 A 0.405358916754 0.08368 ; partial charge def not found CT1x6 12.011000.000 A 0.405358916754 0.08368 ; partial charge def not found CT2x6 12.011000.000 A 0.358141284692 0.234304 ; partial charge def not found CT3x6 12.011000.000 A 0.363486677001 0.326352 ; partial charge def not found H 1 1.0080000.31A 0.0400013524445 0.192464 HA 1 1.0080000.09A 0.235197261589 0.092048 HE1 1 1.0080000.000 A 0.222724679535 0.129704 ; partial charge def not found HE2 1 1.0080000.000 A 0.224506476971 0.108784 ; partial charge def not found HB 1 1.0080000.09A 0.235197261589 0.092048 HC 1 1.0080000.33A 0.0400013524445 0.192464 HP 1 1.0080000.115 A 0.242003727796 0.12552 HR1 1 1.0080000.13A 0.160361769265 0.192464 HR2 1 1.0080000.18A 0.12472582054 0.192464 HR3 1 1.0080000.09A 0.261567863646 0.0326352 HS 1 1.0080000.16A 0.0801808846326 0.4184 #ifdef HEAVY_H HT 1 4.032 0.417 A 0.0400013524445 0.192464 ; CHARMM TIP3p H #else HT 1 1.0080000.417 A 0.0400013524445 0.192464 #endif HA1 1 1.0080000.000 A 0.235197261589 0.092048 ; partial charge def not found HA2 1 1.0080000.000 A 0.238760856462 0.117152 ; partial charge def not found HA3 1 1.0080000.000 A 0.238760856462 0.100416 ; partial charge def not found N 7 14.00700-0.29 A 0.329632525712 0.8368 NC2 7 14.00700-0.80 A 0.329632525712 0.8368 NH1 7 14.00700-0.47 A 0.329632525712 0.8368 NH2 7 14.00700-0.62 A 0.329632525712 0.8368 NH3 7 14.00700-0.30 A 0.329632525712 0.8368 NP 7 14.007000.000 A 0.329632525712 0.8368 ; partial charge def not found NPH 7 14.007000.000 A 0.329632525712 0.8368 ; partial charge def not found NR1 7 14.00700-0.36 A 0.329632525712 0.8368 NR2 7 14.00700-0.70 A 0.329632525712 0.8368 NR3 7 14.00700-0.51 A
[gmx-users] Calculation of dihedral force constants
Dear gmx-users I am trying to calculate dihedral force constants from the diagonal elements in the hessian matrix in internal coordinates. The matrix is given in hartree/rad^2. Upon conversion to kJ/(mol*rad^2) the values seem an order of magnitude higher than I have seen in the force fields (~3.77 kJ/mol for CCCH dihedral but I get ~42 kJ/(mol*rad^2). The conversion I have used is 2625.5 kJ/(mol*hartree) but is there any consideration needed for the angular units? Another thought I had was, The GROMACS dihedral Potential Energy function #1 (eq 4.62) listed in the manual 4.5.4 is Vd=k(1+Cos(nx-x0)) where x is dihedral angle. so the curvature of this function (second derivative) at the minimum is (n^2)*k so do I need to convert my force constants to this function by k_harm /n^2 = k ? Any Help would be greatly appreciated Cody Covington -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
