Re: [gmx-users] Simulation of a charged system

2011-12-07 Thread Mark Abraham
On 8/12/2011 3:21 PM, Surya Prakash Tiwari wrote: Thanks Mark for the reply. I didn't find anything in AMBER manual. I emailed the author of that paper. I have one more question: Whether /charged system correction term/ (-(1/(8*epsilon_0*kappa^2*L^3))*(Sum over q^2)) has been implemented in

Re: [gmx-users] Simulation of a charged system

2011-12-07 Thread Surya Prakash Tiwari
Thanks Mark for the reply. I didn't find anything in AMBER manual. I emailed the author of that paper. I have one more question: Whether *charged system correction term*(-(1/(8*epsilon_0*kappa^2*L^3))*(Sum over q^2)) has been implemented in the PME implementation of Gromacs. I am talking about t

Re: [gmx-users] Simulation of a charged system

2011-12-06 Thread Mark Abraham
On 7/12/2011 11:31 AM, Surya Prakash Tiwari wrote: Dear Gromacs users, I am simulating a charged system with periodic boundary conditions. My system has 506 water molecules and one ion. I am trying to calculate the free energy of an ion. I do not want to use any counter-ions to neutralize the sy

[gmx-users] Simulation of a charged system

2011-12-06 Thread Surya Prakash Tiwari
Dear Gromacs users, I am simulating a charged system with periodic boundary conditions. My system has 506 water molecules and one ion. I am trying to calculate the free energy of an ion. I do not want to use any counter-ions to neutralize the system, because I don't have force-field between my ion