I am using gromos force field fotr my work and This force field's files come filled with LJ functions and now if i want to work with buckingham potential i changed in default section of force field ffG34a21.itp file but it gives me the follwing errors
ERROR 77 [file ffgmxnb.itp, line 144]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) any help appreciated. On Wed, Dec 22, 2010 at 8:40 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > sreelakshmi ramesh wrote: > >> >> so if i set vdwtype =cut off and specify 2 in default section (2 is for >> buck and 1 for LJ ) of topology file will gromacs makes suer that i want the >> calculation with bucking ham potential. >> > > Presumably, since that's what the manual would indicate works. You can > answer these sorts of questions yourself by giving it a try, then verifying > the run parameters by using gmxdump on the resulting .tpr file. > > -Justin > > On Wed, Dec 22, 2010 at 8:32 AM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> sreelakshmi ramesh wrote: >> >> Thanks a lot for timely reply by gmxusers.I read the manual and >> i had altered the buckingham coefficients in topolgy file.Now in >> mdp file in vdwtype i want to specify it as buckingham but looks >> like i can mention only LJ and in manual they haven't told about >> the notation for BJ.any suggestions please. >> >> >> Use of Buckingham potentials is not controlled by the .mdp file, >> except in the fact that several of the vdwtype methods cannot be >> used in conjunction with Buckingham (see manual, section 7.3.11); >> only "cutoff" appears to be viable here. >> >> -Justin >> >> >> sree. >> >> >> On Tue, Dec 21, 2010 at 6:02 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> sreelakshmi ramesh wrote: >> >> can anyone tell me how to alter the parameter B OF >> buckingham >> potential. >> >> >> Manual, chapter 5, especially table 5.4, which specifically >> lists >> all of the parameters and where they are defined. >> >> -Justin >> >> regards, >> sree >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists >
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