Re: Electrostatic interaction of 2 ions

From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri Apr 12 2019 - 10:07:36 CDT

1) do you have switching on? I'm not entirely sure what that does for
electrostatics with the settings you describe.
2) you might also try "fullDirect on"
3) the NAMD value for the Coulombic constant is 332.0636 kcal-A/mol-e^2
4) you don't really need to zero out VDW interactions, since each
interaction type is segregated (see ELECT rather than POTENTIAL)

On Fri, Apr 12, 2019 at 10:35 AM Fateme Ghadirian <
fateme.ghadirian_at_remove_yahoo.com> wrote:

> *Dear NAMD user’s*
>
> *I’m trying to solve a basic and also simple problem with NAMD. It’s about
> just coulombic interaction of sodium and chloride ions and also have a
> comparison between NAMD results and my analytical code with mathematica.*
>
> *So at first I changed the epsilon parameter of their lennard jones
> interactions to zero, in nbfix part of the parameter file, to switch off
> the lennard jones effect, so as a result, VDW energy would be zero through
> time and that is what I’ve expected.*
>
> *But I have 3 questions in this problem:*
>
> *1. As you can see in my .conf file, I’ve defined a cutoff distance of 12
> A and pairlistdist 14 A and set PME to on, so if I choose the first
> distance of the ions like 30 A, this is not right to expect that electrical
> energy should be zero, because of setting PME to on, which calculates full
> electrostatic interaction and there will be no truncation in electrostatic
> energy. But if in the same condition I set PME to off, it is true to get
> zero for electrical interaction, which I’ve got.*
>
> *But setting PME to off causes some problems in the values of elect energy
> calculations; as an example, in the following condition*
>
> *cutoff distance 12 A *
>
> *pairlistdist 14 A*
>
> *PME off*
>
> *First distance of ions: 8Ang (in pdb file)*
>
> *At first time step, with the elect energy formula; kq1q1/r
> (k=332.063711 kcal/mol); elect energy must be -41.5079 kcal/mol, but in the
> log file I have -12.8111 kcal/mol!!!!! When I set PME to on, the right
> answer shows up!*
>
> *The question is, what should I do, not to have full electrostatic
> calculations (I want to have truncation in elect energy upper a certain
> distance between ions), but also have the right value of elect energy?*
>
> *2. I know that in a real problem in NAMD, lennerad jones potential does
> not allow these ions to approach together under a certain distance, and
> also minimization part of the configuration file does not allow atoms to
> take the same places, but as a test, I put the ions at the same position,
> so elect energy must be infinite, and there should be a crash in running
> the program, but I have -1992.3816 kcal/mol elec energy in the log file,
> why is that so?!*
>
> *3. Why sometimes there is a slight difference between log file elect
> energy and analytical calculations kq1q1/r (I’ve checked just first time
> steps)?*
>
> *Some examples:*
>
> *TimeStep 0; r0= 7A : Electrical energy in log file= -47.4445 kcal/mol*
>
> * Electrical energy with analytical formula
> (kq1q1/r) = -47.4376 kcal/mol*
>
>
>
>
> * Some files are attached to the email.*
>
> *Is there anyone who knows the answers of these questions? Would help me a
> lot.*
>
>
>
> *Best Regards,*
>
> *Fateme*
>
>
>
>
>
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Dec 04 2019 - 23:20:43 CST