From: Fateme Ghadirian (fateme.ghadirian_at_yahoo.com)
Date: Fri Apr 12 2019 - 09:33:08 CDT
I’mtrying to solve a basic and also simple problem with NAMD. It’s about justcoulombic interaction of sodium and chloride ions and also have a comparisonbetween NAMD results and my analytical code with mathematica.
So atfirst I changed the epsilon parameter of their lennard jones interactions tozero, in nbfix part of the parameter file, to switch off the lennard joneseffect, so as a result, VDW energy would be zero through time and that is what I’veexpected.
But Ihave 3 questions in this problem:
1. As youcan see in my .conf file, I’ve defined a cutoff distance of 12 A and pairlistdist14 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 ofsetting PME to on, which calculates full electrostatic interaction and therewill be no truncation in electrostatic energy. But if in the same condition Iset PME to off, it is true to get zero for electrical interaction, which I’vegot.
Butsetting PME to off causes some problems in the values of elect energycalculations; as an example, in the following condition
cutoffdistance 12 A
Firstdistance of ions: 8Ang (in pdb file)
At firsttime step, with the elect energy formula; kq1q1/r (k=332.063711 kcal/mol); elect energy mustbe -41.5079 kcal/mol, but in the log file I have -12.8111 kcal/mol!!!!! When Iset PME to on, the right answer shows up!
Thequestion is, what should I do, not to have full electrostatic calculations (Iwant to have truncation in elect energy upper a certain distance between ions),but also have the right value of elect energy?
2. I knowthat in a real problem in NAMD, lennerad jones potential does not allow theseions to approach together under a certain distance, and also minimization partof the configuration file does not allow atoms to take the same places, but asa 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 -1992.3816kcal/mol elec energy in the log file, why is that so?!
3. Whysometimes there is a slight difference between log file elect energy andanalytical calculations kq1q1/r (I’ve checked just first time steps)?
TimeStep0; r0= 7A : Electrical energy in log file= -47.4445kcal/mol
Electrical energy with analytical formula(kq1q1/r) = -47.4376 kcal/mol
Some files are attached to the email.
Is there anyonewho knows the answers of these questions? Would help me a lot.
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