[gmx-users] some code for writing topologies

All, Below is some code I wrote a few years ago during my PhD. I started with a list of bonds in a file called 'bonds' and t he used this list to automatically create the lists of angled and proper dihedrals. I went on to edit this code to create a topology for entire polymers based on a single

RE: [gmx-users] setting up a simulation of an ionic liquid

usually get an system with converged density, which I finally equilibrated for further 5-10ns. Cheers, Flo * Laura Leay [2013-05-14 09:13:55 +]: >Thanks for the help Justin, > >I've taken a look at the atom with the maximum force using VMD and I can't see >anything wron

RE: [gmx-users] setting up a simulation of an ionic liquid

users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 13 May 2013 23:05 To: Discussion list for GROMACS users Subject: Re: [gmx-users] setting up a simulation of an ionic liquid On 5/13/13 11:50 AM, Laura Leay wrote: > All, > > I

[gmx-users] setting up a simulation of an ionic liquid

All, I've seen a few threads about simulations in ionic liquds but have not come across anything that tells me what settings I should use in my mdp file. The system is nitric acid which has fully dissociated into NO3- and HO3+. The simulation will run fine with just the ions at low density unde

[gmx-users] Residue renaming during mdrun

All, I have a system of nitric acid modelled as NO3- and HO3+ plus SPC water. After setting the system up using genbox I then energy minimise. Althouth the input conf.gro file looks fine (NO3- labelled 'NO3', HO3+ labelled 'HO3' and water labelled 'SOL') the confout file has all of the H3O renam

[gmx-users] Some notes on parameterising dreiding

It took me quite a while to get to grips with this and, since the question was asked about a year ago by someone else with no response, I thought I'd share my insight. LJ potentials: Its important to note the slight difference from the widely used form. You need to convert Ro to sigma by divid

RE: [gmx-users] Dihedral form

...@gromacs.org] on behalf of Erik Marklund [er...@xray.bmc.uu.se] Sent: 15 November 2012 13:37 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Dihedral form You could shift the reference angle by pi, which changes the sign of the cosine. Best, Erik 15 nov 2012 kl. 14.25 skrev Laura

[gmx-users] Dihedral form

All, I would like to parameterise the Dreiding force field for use with Gromacs. One thing I am not sure about is how to parameterise the dihedrals The Dreiding paper has the form; E= 0.5k { 1 - cos[ n( phi - phi_o)]} However I cannot find this form in the Gromacs manual. The closest I can fi

Re: [gmx-users] Tabulated potential segmentation fault

On Fri, 2012-04-13 at 11:01 +1000, Mark Abraham wrote: > On 13/04/2012 2:48 AM, Laura Leay wrote: > > All, > > > > I'm trying to run a tabulated soft core potential with the form V = > > A + Br^2 + Cr^3 up to about r=0.1 A and the normal LJ 6-12 potential >

[gmx-users] Tabulated potential segmentation fault

All, I'm trying to run a tabulated soft core potential with the form V = A + Br^2 + Cr^3 up to about r=0.1 A and the normal LJ 6-12 potential after this. I've chosen the parameters of this equation to be the same for all atoms in my system (a polymer containing carbon, nitrogen and hydrogen). I

[gmx-users] Tabulated potentials

All, I'm simulating a very small system of methane using tabulated potentials. Charges are not modified and I'm using a cubic for values up to 0.19 nm and the normal 6-12 LJ potential after that (the form the cubic is such that the value and gradient at 0.19 nm is the same as for the 6-12 LJ).

[gmx-users] Surface area calculation

Can anyone explain in detail the method that gromacs uses to calculate surface area? Which surface area is it calculating (e.g., connolley, accessible)? I am under the impression that the final result is given in nm^2. Is this correct? Carrying out the surface area calculation in gromacs using t