[gmx-users] solvent orientation/sorient

I want to calculate solvent orientation around two types of spherical particle. The solvent has a long alkyl chain. I use sorient with three atoms in the carbon chain in my index group, one at each end and one in the middle. The results are confusing me. Theta_1 is described as "the angle with

[gmx-users] LJ-SR and LJ-14

If you want the "total" Lennard-Jones potential between two groups, would you simply add LJ-SR + LJ-14? If so, what is the utility of calculating both potentials separately? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] g_order

th the arguments but nothing I try seems to make a difference. What am I doing wrong? - Stella Nickerson -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mai

Re: [gmx-users] g_order

and it always tells me that's an "invalid command line argument." On Thu, Sep 10, 2015 at 1:44 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/10/15 1:58 PM, Stella Nickerson wrote: > >> I have a molecule with a carbon chain attached to a ring. I want to use >

Re: [gmx-users] OPLS forcefield amide charge

Thanks! On Fri, Aug 28, 2015 at 9:57 AM, Pallavi Banerjee pallavis...@students.iiserpune.ac.in wrote: Hey. I am extremely sorry about the incorrect reference. I should have been careful. You should find the right charges in the supporting information of the following paper.

[gmx-users] OPLS forcefield amide charge

I am simulating a polymer using the OPLS forcefield. The polymer has a sidechain with a secondary amide. Using the atom charges given in the forcefield, the amide group (N, O, 2Cs, 2 Hs) has a net negative charge. I don't understand why this is so, since to my knowledge amides are not generally

[gmx-users] OPLS and GROMOS forcefields

Hi, I'm simulating a polymer dissolved with an ionic liquid. Would it be possible to use the OPLS forcefield for the solvent and the GROMOS forcefield for the particle, or would that result be inherently meaningless? Thanks, Stella -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Lumping different molecule types together as rest

I'm simulating a system with four different types of molecules. When I try to look at the energies between different types of molecules, it only lists two of the types, and lumps the other two together as rest. As in BMI-rest. Why is this happening? Thanks, Stella -- Gromacs Users mailing list

[gmx-users] How to exclude atoms within the same molecule from an rdf.

I'm simulating a mixture of molecules (call them Molecules A, B, and C). The rdf between A and B and between A and C both look fine, but the one between A and A is crazy-looking. I assume this is because it's comparing atoms within the same molecule. I can't figure out how to exclude atoms in the

[gmx-users] g_spatial

I am simulating an ionic liquid, and I want to generate a spatial density map on the anion around the cation. I want an image that looks like this:

[gmx-users] Spacial density map

I am simulating an ionic liquid, and I want to generate a spatial density map on the anion around the cation. I want an image that looks like this:

Re: [gmx-users] Pull code with dummy atom as reference - not working

to figure out another way to generate a PMF. Thanks again! On Wed, Jul 23, 2014 at 1:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/23/14, 4:04 PM, Stella Nickerson wrote: I want to pull a carbon particle (170 atoms in a lattice) across an interface between Liquid A and Liquid B

[gmx-users] Pull code with dummy atom as reference - not working

I want to pull a carbon particle (170 atoms in a lattice) across an interface between Liquid A and Liquid B. The particle starts out in Liquid A with the center of mass at about x = 2.5 y = 2.5 z = 2.5. The liquid-liquid interface is at about z = 5. I want to pull the particle in a straight