Hi,
So if I use PME for coloumb interactions, then what are my options? Would you then suggest breaking up the 12-atom charge grp in the arginine residue into 2 charge groups? Would it be enough to make the changes in the .rtp or parameters in other files must be changed? POoja On Sat, Jul 17, 2010 at 11:16 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Sai Pooja wrote: > >> A charge grp consisting of 12 atoms is created from Arginine residues in >> my topology file. >> ; residue 14 ARG rtp ARG q +1.0 >> 476 NH1 14 ARG N 150 -0.47 14.007 ; >> qtot -3.47 >> 477 H 14 ARG HN 150 0.31 1.008 ; >> qtot -3.16 >> 478 CT1 14 ARG CA 150 0.07 12.011 ; >> qtot -3.09 >> 479 HB 14 ARG HA 150 0.09 1.008 ; >> qtot -3 480 CT2 14 ARG CB 151 -0.18 >> 12.011 ; qtot -3.18 481 HA 14 ARG HB1 151 >> 0.09 1.008 ; qtot -3.09 >> 482 HA 14 ARG HB2 151 0.09 1.008 ; >> qtot -3 483 CT2 14 ARG CG 152 -0.18 >> 12.011 ; qtot -3.18 484 HA 14 ARG HG1 152 >> 0.09 1.008 ; qtot -3.09 485 HA 14 ARG HG2 152 >> 0.09 1.008 ; qtot -3 486 CT2 14 ARG CD >> 153 0.2 12.011 ; qtot -2.8 487 HA 14 ARG >> HD1 153 0.09 1.008 ; qtot -2.71 >> 488 HA 14 ARG HD2 153 0.09 1.008 ; >> qtot -2.62 >> 489 NC2 14 ARG NE 153 -0.7 14.007 ; >> qtot -3.32 >> 490 HC 14 ARG HE 153 0.44 1.008 ; >> qtot -2.88 >> 491 C 14 ARG CZ 153 0.64 12.011 ; >> qtot -2.24 >> 492 NC2 14 ARG NH1 153 -0.8 14.007 ; >> qtot -3.04 >> 493 HC 14 ARG HH11 153 0.46 1.008 ; >> qtot -2.58 >> 494 HC 14 ARG HH12 153 0.46 1.008 ; >> qtot -2.12 >> 495 NC2 14 ARG NH2 153 -0.8 14.007 ; >> qtot -2.92 >> 496 HC 14 ARG HH21 153 0.46 1.008 ; >> qtot -2.46 >> 497 HC 14 ARG HH22 153 0.46 1.008 ; >> qtot -2 498 C 14 ARG C 154 0.51 >> 12.011 ; qtot -1.49 >> 499 O 14 ARG O 154 -0.51 15.999 ; >> qtot -2 >> See charge group 153. It has 12 atoms. This is true for all Arginine >> residues. It seems that charge groups must have an integer net-charge. As >> you can see, it assigns charge grps 151, 152, 153 etc. till the net-charge >> becomes an integer. >> >> > > Strictly speaking, charge groups do not always have to have a net charge, > but generally they do. > > > One option would be to manually make them. In this case, I could simply >> breakdown this particular charge grp into 2 smaller chargegrps but I am sure >> if that would be consistent with the forcefield and not sure if it would be >> possible to set the net charge to an integral value to an integer for the >> smaller charge groups. >> > > Simply breaking the charge group apart seems too arbitrary. If you're not > using PME (which you're not), then you need integral charge groups, so it > looks like this one has to stay intact. It just seems like there's the > potential for inaccurate short-range interactions when the entire sidechain > is encompassed by a single charge group. Perhaps for your case it will not > matter so much; maybe someone else can comment. There are numerous threads > in the list archive discussing this situation, so I won't repeat all of that > here. > > > Also, is there an alternate way by changing the Cut-off? >> >> > Not really. Any cutoff you choose might be affected by artifacts of a > large charge group. > > -Justin > > Any thoughts? >> Pooja >> >> >> >> Pooja >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Quaerendo Invenietis-Seek and you shall discover.
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