[gmx-users] Constraint bonds and contribution to pressure

Dear all I am simulating simple bead-rod polymer chains, so I apply constraints to all the bonds of my system using the p-lincs algorithm. I try to understand how do the constraint forces contribute to the pressure of the system, but I am a bit confused. Can anyone help? Regards, Tommy -- gmx-

Re: [gmx-users] vdw-modifier in GROMACS 4.6.1.

work? Does it differ from > vdw-type= Switch > vdw-modifier=None? > > Mark > > > On Thu, Apr 11, 2013 at 2:13 PM, Chrisostomos Batistakis < > tomyvanba...@gmail.com> wrote: > > > Dear all > > > > I have started simulations with the GROMACS 4.6.1, bu

[gmx-users] vdw-modifier in GROMACS 4.6.1.

Dear all I have started simulations with the GROMACS 4.6.1, but I am bit confused with the application of the vdw-modifier. As far as I understand, in the case of : vdw-type= cut-off vdw-modifier-Potential-Shift the result will be a LJ potential shifted by a constant in order to be zero at the c

Re: [gmx-users] Van der waals types

Dear Mark Many thanks for your responces. Yes, of course I have seen that. But what I am asking is if when using * vdw-type=cut-off* the potential is shifted acoording to the following equation: VLJ=V(r)-V(rc) for rwrote: > > > On 11/04/12, *Chrisostomos Batistakis * wrote: >

Re: [gmx-users] Van der waals types

Dear Mark I have already checked both sections but I don't understand.. That's why I am asking for help :-) On Wed, Apr 11, 2012 at 12:18 PM, Mark Abraham wrote: > On 11/04/12, *Chrisostomos Batistakis * wrote: > > Dear all > > I am looking in the manual but I don'

[gmx-users] Van der waals types

Dear all I am looking in the manual but I don't understand... When using *vdw-type =cut-off* in the .mdp file, is the LJ potential only truncated in the cut-off distance rc, or is it also shifted in order to avoid discontinuity when rij=rc ? If no, how can I have a shifted and truncated LJ pote

Re: [gmx-users] g_energy for density calculation

On Fri, Feb 3, 2012 at 2:38 PM, Mark Abraham wrote: > On 4/02/2012 12:34 AM, Chrisostomos Batistakis wrote: > > Dear all > > I would like to calculate the total density vs time in my system during an > NPT simulation. I read the manual that I have to use the g_energy comman