Thank you Dr. Justin. With the value of kb, if the unit is KJ/mol nm^2 then the value is obtained as 624982.
1mDyne/A is 60230KJ/mol nm^2 kb value for f2 molecule from gaussian is 10.3766 On Wed, Aug 1, 2018 at 12:20 AM, Justin Lemkul <[email protected]> wrote: > > > On 7/31/18 2:48 PM, RAHUL SURESH wrote: > >> 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) >> > > Here's your problem. GROMACS uses SI units. Presumably you've listed the > b0 value in Angstrom, when it should be in nm. Note how your value is 10x > larger than anything else in the file. Check the units on kb, as well. > > -Justin > > > 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]. >>> >>> > -- > ================================================== > > 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].
