Re: [gmx-users] buckingham potentials

--- On Wed, 12/22/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] buckingham potentials To: "Gromacs Users' List" Date: Wednesday, December 22, 2010, 8:04 AM sreelakshmi ramesh wrote: > Dear justin, >                    I have no clues  ab

Re: [gmx-users] buckingham potentials

Dear justin, since i am rewritting a force field i am able to write the c6 and c12 parameter in force field file but how to do i declare the parameter B of bucking ham equation .Wat notation should i use for declaring it in force field file.The parameter C is declared as c6 and A

Re: [gmx-users] buckingham potentials

sreelakshmi ramesh wrote: Dear justin, I have no clues about rewriting a force field so i think i can t proceed with this anymore. thanks a lot for your patient reply. For the future, you will waste a lot less time (your own, and that of those who are trying to help yo

Re: [gmx-users] buckingham potentials

Dear justin, I have no clues about rewriting a force field so i think i can t proceed with this anymore. thanks a lot for your patient reply. sree. On Wed, Dec 22, 2010 at 9:32 AM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> Dear justin, >>

Re: [gmx-users] buckingham potentials

sreelakshmi ramesh wrote: Do u mean to say that all the force fields available in gromacs are default to be used only for LJ potential. Yes. That's why they all have their [defaults] directives set to use LJ. -Justin On Wed, Dec 22, 2010 at 9:32 AM, Justin A. Lemkul

Re: [gmx-users] buckingham potentials

Do u mean to say that all the force fields available in gromacs are default to be used only for LJ potential. On Wed, Dec 22, 2010 at 9:32 AM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> Dear justin, >> I am sorry the file is ffG43a1nb.itp.It < >> http://ffG43a1n

Re: [gmx-users] buckingham potentials

sreelakshmi ramesh wrote: Dear justin, I am sorry the file is ffG43a1nb.itp.It was a typing mistake. The points I raised before still stand: 1. You're not using 43A1, you're using ffgmx, according to that message from grompp. 2. You can't make

Re: [gmx-users] buckingham potentials

Dear justin, I am sorry the file is ffG43a1nb.itp.It was a typing mistake. On Wed, Dec 22, 2010 at 9:26 AM, Justin A. Lemkul wrote: > > > Justin A. Lemkul wrote: > >> >> >> sreelakshmi ramesh wrote: >> >>> I am using gromos force field fotr my work and This force field's files >

Re: [gmx-users] buckingham potentials

Justin A. Lemkul wrote: sreelakshmi ramesh wrote: 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 fo

Re: [gmx-users] buckingham potentials

sreelakshmi ramesh wrote: 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 [

Re: [gmx-users] buckingham potentials

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]: Try

Re: [gmx-users] buckingham potentials

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 ans

Re: [gmx-users] buckingham potentials

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. On Wed, Dec 22, 2010 at 8:32 AM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> Thanks a lot f

Re: [gmx-users] buckingham potentials

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 nota

Re: [gmx-users] buckingham potentials

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 plea

Re: [gmx-users] buckingham potentials

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 -- Ju

[gmx-users] buckingham potentials

can anyone tell me how to alter the parameter B OF buckingham potential. regards, sree -- gmx-users mailing listgmx-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 do