Dear Gromacs Users!
I want to perform in vacuum simulation for the simple peptid parametrised by Amber 99SB and Gromos 43.1 force fields. As I understoon the primary foal of in vacum simulation in the turn of all charges in the residues wich are not exposed to the solvent. >From topology file ( done by Amber) I've found such example for the Gly residue as well for charged Glu ; residue 404 GLY rtp GLY q 0.0 6365 N 404 GLY N 6365 -0.4157 14.01 ; qtot -1.848 6366 H 404 GLY H 6366 0.2719 1.008 ; qtot -1.576 6367 CT 404 GLY CA 6367 -0.0252 12.01 ; qtot -1.601 6368 H1 404 GLY HA1 6368 0.0698 1.008 ; qtot -1.531 6369 H1 404 GLY HA2 6369 0.0698 1.008 ; qtot -1.461 6370 C 404 GLY C 6370 0.5973 12.01 ; qtot -0.8642 6371 O 404 GLY O 6371 -0.5679 16 ; qtot -1.432 ; residue 28 GLU rtp GLU q -1.0 354 N 28 GLU N 354 -0.5163 14.01 ; qtot -2.516 355 H 28 GLU H 355 0.2936 1.008 ; qtot -2.223 356 CT 28 GLU CA 356 0.0397 12.01 ; qtot -2.183 357 H1 28 GLU HA 357 0.1105 1.008 ; qtot -2.073 358 CT 28 GLU CB 358 0.056 12.01 ; qtot -2.017 359 HC 28 GLU HB1 359 -0.0173 1.008 ; qtot -2.034 360 HC 28 GLU HB2 360 -0.0173 1.008 ; qtot -2.051 361 CT 28 GLU CG 361 0.0136 12.01 ; qtot -2.038 362 HC 28 GLU HG1 362 -0.0425 1.008 ; qtot -2.08 363 HC 28 GLU HG2 363 -0.0425 1.008 ; qtot -2.123 364 C 28 GLU CD 364 0.8054 12.01 ; qtot -1.317 365 O2 28 GLU OE1 365 -0.8188 16 ; qtot -2.136 366 O2 28 GLU OE2 366 -0.8188 16 ; qtot -2.955 367 C 28 GLU C 367 0.5366 12.01 ; qtot -2.418 368 O 28 GLU O 368 -0.5819 16 ; qtot -3 My qustions: 1- What is difference between charge value and charge B qtot value ? 2- Must I turn off absolutely all charges even in the non-polar residues e.g edit -0.3662 value to the 0.0000 for all atoms in Gly for instance. ? What another edition should I do for the elimination of the charges ? 3- I've found that GROMOS force field is not good choise for the vacum simulation because of non condensive phase of that system but in some works authors use this ff for in vacum system. What should I do for the adaptation of that ff for my system? Thanks James
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