Re: [gmx-users] REMD using Gromacs 3.2.1

Thanks all. I think it is not there as -replex is not implemented in mdrun-3.2.1 Regards, Monika Mark Abraham wrote: Monika wrote: Dear All, I have one query regarding usage of version 3.2.1 of GROMACS for replica exchange. I could not find any mention at the 3.2 manual for replica exchange,

Re: [gmx-users] REMD using Gromacs 3.2.1

Monika wrote: Dear All, I have one query regarding usage of version 3.2.1 of GROMACS for replica exchange. I could not find any mention at the 3.2 manual for replica exchange, as I could find for version 3.3 and above. For eg., by using -replex option. So how can one perform replica exchange u

Re: [gmx-users] REMD using Gromacs 3.2.1

It looks from the update history (http://www.gromacs.org/content/view/18/132/) that REMD is a new feature as of version 3.3. -Justin Quoting Monika <[EMAIL PROTECTED]>: > Dear All, > I have one query regarding usage of version 3.2.1 of GROMACS for replica > exchange. I could not find any mention

[gmx-users] REMD using Gromacs 3.2.1

Dear All, I have one query regarding usage of version 3.2.1 of GROMACS for replica exchange. I could not find any mention at the 3.2 manual for replica exchange, as I could find for version 3.3 and above. For eg., by using -replex option. So how can one perform replica exchange using 3.2.1? Is

Re: [gmx-users] Brownian dynamics

Yin Jian wrote: Hi Mark, Thanks for the message. But the friction is just I want to add in. The dipole of the water I may use the dielectric constant to mimic its screening. So I donot Think the information on this page helpful. What is its vacuum? The model of water is just three LJ balls and a

RE: [gmx-users] Brownian dynamics

Hi Mark, Thanks for the message. But the friction is just I want to add in. The dipole of the water I may use the dielectric constant to mimic its screening. So I donot Think the information on this page helpful. What is its vacuum? The model of water is just three LJ balls and a dipole, right? A

Re: [gmx-users] Brownian dynamics

Yin Jian wrote: Hi Berk, I am looking for a way to be able to run MD faster without Explicit solvent component. Brownian dynamics (I mean langevin Dynamics) is way out I think. But I am not sure the package Implemented in Gromacs is a good one or not yet. Since I have Seen no one using it in the

[gmx-users] Brownian dynamics

Hi Berk, I am looking for a way to be able to run MD faster without Explicit solvent component. Brownian dynamics (I mean langevin Dynamics) is way out I think. But I am not sure the package Implemented in Gromacs is a good one or not yet. Since I have Seen no one using it in the literature yet, ri