Hi, On Wed, Sep 9, 2015 at 7:55 PM Phwey Gil <ps...@case.edu> wrote:
> Hi Justin, Maryam, > > My initial problem was that I did not specify the atom types as Justin > said. Now I am able to change the masses and charges easily, but there are > still some problems with implementing the lennard-jones potential. > > In my .itp file I write: > [ atomtypes ] > X 1 7.777 0.450 A 2 3 > > Where X is the atom in question, and I have made up numbers to see how they > appear in topol.tpr. I was able to see that the masses and charges can be > implemented straightforwardly. However, the C6 and C12 parameters are not > (2 and 3). The output values found in topol.tpr are: > > functype[9]=LJ_SR, c6= 1.41771114e+00, c12= 3.59777004e-01 > LJ parameters for the two atom types involved in an interaction combine according to the equations in chapter 4 of the manual. There's been some pre-computation already. Additionally, [ Bonds ] do not appear in the topol.tpr either. > Well, don't ask grompp to convert your bonds into constraints ;-) Mark > On Wed, Sep 9, 2015 at 7:43 AM, Maryam Kowsar <maryam.kow...@gmail.com> > wrote: > > > Hi justin > > Actually i modified the forcefield parameters to introduce atoms that are > > not present in that. I think you are right in the case that we want to > > change bonded or nonbonded parameters in the forcefield > > > > On Wednesday, September 9, 2015, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > On 9/9/15 7:29 AM, Maryam Kowsar wrote: > > > > > >> Hi dan > > >> I think that's not possible to change forcefield parameters and use > the > > >> old > > >> defined forcefield like opls. When you change the parameters in .itp > you > > >> should introduce your own forcefield. Try to have all the needed files > > of > > >> forcefield in a new folder and use that during making topology. > > >> > > >> > > > This is not true. Any force field can be modified or extended. A local > > > copy of a modified force field is a safe recommendation, but in the > case > > of > > > simply adding new atom types, there's little harm that can be done. > > > > > > -Justin > > > > > > On Tuesday, September 8, 2015, Phwey Gil <ps...@case.edu> wrote: > > >> > > >> Hi, > > >>> > > >>> I am looking to specify my own parameters for LJ parameters. Using > the > > >>> OPLS > > >>> forcefield, I only want to change the LJ parameters of some atoms. > > >>> > > >>> I have H2O, C8H16O2 (Octanoic acid) and C2H6O (Ethanol). > > >>> I am using SPC/E for H2O, and OPLS for C8H16O2 and C2H6O. And I want > to > > >>> change the LJ parameters for the hydrogens in C8H16O2 only. > > >>> > > >>> I have tried specifying [ atomtypes ] in various places (In .top or > > .itp) > > >>> using the following format: > > >>> > > >>> [ atomtypes ] > > >>> H H 1.008 0.450 A 5.66387665E-4 > > >>> 2.80730518E-7 > > >>> > > >>> But I was not successful; I checked topol.tpr and the numbers are > > >>> according > > >>> to OPLS and not my specified values. > > >>> > > >>> Can someone give me advice on how to do this? I've checked the forums > > >>> and I > > >>> was not successful at finding the correct information. > > >>> > > >>> Best Regards, > > >>> > > >>> Dan > > >>> > > >>> -- > > >>> Dan Gil > > >>> Case Western Reserve University | Class of 2016 > > >>> Researcher, Department of Chemical Engineering > > >>> ps...@case.edu <javascript:;> > > >>> -- > > >>> 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 <javascript:;>. > > >>> > > >>> > > > -- > > > ================================================== > > > > > > Justin A. Lemkul, Ph.D. > > > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > > > > Department of Pharmaceutical Sciences > > > School of Pharmacy > > > Health Sciences Facility II, Room 629 > > > 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. > > > > > > -- > Dan Gil > Case Western Reserve University | Class of 2016 > Researcher, Department of Chemical Engineering > ps...@case.edu > -- > 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.
