On Tue, 31 Jul 2018 at 11:38 PM, Justin Lemkul <[email protected]> wrote:
> > > On 7/31/18 2:05 PM, RAHUL SURESH wrote: > > Hi Dr. Mark > > > > The itp file is as follows. > > > > [ moleculetype ] > > ; Name nrexcl > > FLU1 3 > > > > [ atoms ] > > ; nr type resnr residue atom cgnr charge mass > > typeB chargeB massB > > 1 opls_786 1 FLU1 F 0 0 > > 18.99840 > > 2 opls_786 1 FLU1 F 0 0 > > 18.99840 > > > > [ bonds ] > > ; ai aj funct > > 1 2 1 ; F F > > What parameters have you assigned for this bond? If you are asking in ffbonded.itp, then F F 1.43363 351456( which I got from previously existing data) What is the unit for harmonic force constraint (kB) in ffbonded.itp? The kb value got from vibrational freq analysis is 10.3766 mDyne per Angstrom I haven’t added any other parameters to any of the file in Gromacs > > > > [ pairs ] > > ; ai aj funct > > 1 2 > > Why are you assigning a pair interaction? These are for 1-4 > interactions. If you're adding a pair, you're going to get a huge LJ > repulsion between your atoms that overwhelms the bonded potential, which > may be the cause of your problem. > > -Justin Yea got it Justin. I will correct it.! > > > > [ angles ] > > ; ai aj ak funct > > > > [ dihedrals ] > > ; ai aj ak al funct > > > > The atom type is chosen based on the sigma and epsilon values from the > > paper attached to previous mail. [ pre-existing atom type ] > > > > The atom didnt move much further but on equilibration the atoms are > totally > > dispersed. > > > > > > > > On Tue, Jul 31, 2018 at 10:58 PM, Mark Abraham <[email protected] > > > > wrote: > > > >> Hi, > >> > >> We can't tell without seeing your molecule type for F2. Presumably > there is > >> no bond or the bond is too weak. How far do they move apart? > >> > >> Mark > >> > >> On Tue, Jul 31, 2018, 14:49 RAHUL SURESH <[email protected]> > wrote: > >> > >>> Hi. > >>> > >>> I obtained the LJ parameters from the paper > *10.1007/s10765-009-0624-0. [ > >>> OPLS_786 ]* > >>> > >>> Add the bond length and harmonic constraints from in ffbonded.itp > >>> > >>> The charge is changed to 0 in the itp file and added to .top file. > >>> > >>> Minimizations are executed without any error. But on examining the gro > >> file > >>> from minimization, the fluorine molecules are broken into atoms. [ ie > >> they > >>> atoms move away ] > >>> > >>> Why is this happening? > >>> > >>> > >>> On Mon, Jul 30, 2018 at 6:17 PM, Justin Lemkul <[email protected]> > wrote: > >>> > >>>> > >>>> On 7/30/18 5:54 AM, RAHUL SURESH wrote: > >>>> > >>>>> Hello users. > >>>>> > >>>>> I overcame the warning errors. The naming is correct now. I tried to > >>>>> update > >>>>> the parameters for ffbonded.itp but how will I find the Kb value for > >>> F-F ? > >>>> Vibrational frequency analysis. > >>>> > >>>> Be careful generating the topology in the manner you have; the F > >>>> parameters come from trifluoroethanol, so the LJ parameters may not be > >>> what > >>>> you want. And the charge of both F atoms in F2 should be set to zero > >>> (note > >>>> that TopolGen is a dumb script that just looks for similarity; the > >>>> resulting topologies often require lots of changes). > >>>> > >>>> -Justin > >>>> > >>>> On Sat, 28 Jul 2018 at 6:52 PM, RAHUL SURESH <[email protected] > > > >>>>> wrote: > >>>>> > >>>>> Hi all > >>>>>> I am performing a simulation between a protein and Fluorine > >> molecule. I > >>>>>> have optimized the F2 structure using Gaussian and inserted into the > >>> box > >>>>>> using gmx insert-molecules command after adding solvent [gmx > >> solvate]. > >>>>>> The > >>>>>> topology for fluorine molecule is generated by topolgen. > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> *[ moleculetype ]; Name nrexclFLU1 3[ > atoms > >>> ]; > >>>>>> nr type resnr residue atom cgnr charge mass > >> typeB > >>>>>> chargeB massB 1 opls_164 1 FLU1 F 0 > >>>>>> -0.206 18.99840 2 opls_164 > >> 1 > >>>>>> FLU1 F 0 -0.206 18.99840 > >> [ > >>>>>> bonds ]; ai aj funct 1 2 1 ; F F[ pairs ]; > >>> ai > >>>>>> aj funct[ angles ]; ai aj ak funct[ dihedrals ]; ai aj > >> ak > >>>>>> al funct* > >>>>>> > >>>>>> > >>>>>> On command gmx grompp -f em.mdp -c alz_F.gro -p alz.top -o ions.tpr > >> i > >>>>>> get > >>>>>> the following errors > >>>>>> > >>>>>> > >>>>>> *ERROR 1 [file fluorine.itp, line 21]: No default Bond types* > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> *NOTE 1 [file alz.top, line 5915]: System has non-zero total > charge: > >>>>>> -23.600000 Total charge should normally be an integer. See > >>>>>> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > >>>>>> <http://www.gromacs.org/Documentation/Floating_Point_Arithmetic> > >> for > >>>>>> discussion on how close it should be to an integer.* > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> *WARNING 1 [file alz.top, line 5915]: 16639 non-matching atom names > >>>>>> atom > >>>>>> names from alz.top will be used atom names from alz_F.gro will be > >>>>>> ignored* > >>>>>> > >>>>>> > >>>>>> Indeed there are only 628 atoms in .top file. > >>>>>> > >>>>>> Any suggestions? > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> -- > >>>>>> *Regards,* > >>>>>> *Rahul * > >>>>>> > >>>>>> > >>>> -- > >>>> ================================================== > >>>> > >>>> Justin A. Lemkul, Ph.D. > >>>> Assistant Professor > >>>> Virginia Tech Department of Biochemistry > >>>> > >>>> 303 Engel Hall > >>>> 340 West Campus Dr. > >>>> Blacksburg, VA 24061 > >>>> > >>>> [email protected] | (540) 231-3129 > >>>> http://www.thelemkullab.com > >>>> > >>>> ================================================== > >>>> > >>>> -- > >>>> 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 [email protected]. > >>>> > >>> > >>> > >>> -- > >>> *Regards,* > >>> *Rahul * > >>> -- > >>> 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 [email protected]. > >>> > >> -- > >> 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 [email protected]. > >> > > > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > [email protected] | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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 [email protected]. > -- *Regards,* *Rahul * -- 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 [email protected].
