[gmx-users] How to define (or modify) a new potential function in Gromacs?

Dear Gromacs community, I am attemping to use Gromacs for a Coarse - grained simulation. In our model, we have a term similar to the angle harmonic potential term, but the variable is not angle but the volume created by three consecutive vectors. I don't know if there is a way to implement that

[gmx-users] ATOMTYPES directive

Dear Gromacs community, In the [ atomtypes ] directive, according to Gromacs manual, it should have 7 seperated fields, which are name, at.num, mass, charge, ptype, c6, c12. However, when I remove the field of at.num, Gromacs still works without notifying any error. If I insert 2 fields more, it

[gmx-users] Exclusion - determine neighboring atoms by atom indices or by bond connections?

Dear Gromacs community, In the Gromacs manual, if nrexcl = 3, that means atoms i+1, i+2, i+3 are excluded from non-bonded interactions with atom i. I don't know how Gromacs determine the neighboring atoms, based on atom indices or bond connections? For example, if I have a simple connection

[gmx-users] Exchange temperature instead of exchange coordinate in replica exchange molecular dynamics?

Hi all, I am reading the paper "Replica-exchange molecular dynamics method for protein folding" by Yuko Okamoto. In this paper, they exchange temperatures of 2 replica. To evaluate that replica exchange is successful, they calculate exchange probability; plot the temperature, potential energy per

[gmx-users] Dihedral angle parameters in Gromacs and Amber

*Dear Gromacs society,* *I don't know how Gromacs define and calculate the multiplicity and equilibrium dihedral angle? For example, in Amber, the multiplicity is 1 and -3 but in Gromacs it is 1 and 3; All phi0 values in gromacs are positive but they are negative in Amber.* *Thank you very much

Re: [gmx-users] Space between the columns in the topology file of Gromacs

Thank you, Best, *Lan Hoa* 2017-06-15 17:02 GMT-05:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > Those are simply fields separated by whitespace. Columns not relevant. > > Mark > > On Thu, 15 Jun 2017 22:10 lan hoa Trinh <trinhlan...@gmail.com> wrote:

[gmx-users] Space between the columns in the topology file of Gromacs

Dear Gromacs society, I wonder if there is the default for the space between the columns in the topology file, for example: [ bonds ] ;ai aj funcr0(nm) Kb 12 1 3.805916447e-01 2.0e+04 23 1 3.788218579e-01 2.0e+04 3

Re: [gmx-users] Topology file and itp file

awesome :) Thank you! *Lan Hoa* 2017-04-23 20:15 GMT-05:00 Justin Lemkul <jalem...@vt.edu>: > > > On 4/22/17 10:39 PM, lan hoa Trinh wrote: > >> Dear Justin, >> I am assessing based on a time series. You are right :), even I used the >> same topology file, t

Re: [gmx-users] Topology file and itp file

ngle point, it is not true when we try to simulate over a period of time and what we can trust is the the average value. Hum, do I understand wrongly again, hixx. Best regards, *Lan Hoa* 2017-04-22 20:41 GMT-05:00 Justin Lemkul <jalem...@vt.edu>: > > > On 4/22/17 9:06 PM,

Re: [gmx-users] Topology file and itp file

Justin Lemkul <jalem...@vt.edu>: > > > On 4/20/17 4:37 PM, lan hoa Trinh wrote: > >> Dear Mark, >> I equilibrated my system in NVT, and then plot the potential energy. >> However the potential energy created with the two topology is not match. >> Thanks in

Re: [gmx-users] Topology file and itp file

e you assessing "different?" > > Mark > > On Thu, 20 Apr 2017 21:13 lan hoa Trinh <trinhlan...@gmail.com> wrote: > > > Dear All, > > I am modelling a system of spherical beads (which I named as Fi) which > only > > repulsive each other. I would h

[gmx-users] Topology file and itp file

Dear All, I am modelling a system of spherical beads (which I named as Fi) which only repulsive each other. I would highly appreciate if some one can have a look at the following topology which I created: (ficoll1.top) [ defaults ] ;nbfunc comb-rule gen-pairs 1 1 no [

[gmx-users] Generate non-bonded combinations

Dear Gromacs community, I am using Gromacs to simulate a C-alpha structure and have the following topology file (created by http://smog-server.org/). [ defaults ] ;nbfunc comb-rule gen-pairs 1 1 no [ atomtypes ] ;name mass charge ptype c10 c12 CA 1.000