[gmx-users] Question about umbrella sampling "pull-geometry" option

Dear GMXers, I'm running umbrella PMF calculations using GROMACS 4.5. A molecule is placed at various locations of a channel to compute the energy barrier of the entrance. Below is the PMF section of mdp input, to compute the PMF around the position of (4.04700, 4.0582, -2.2058). The pulling mole

[gmx-users] Question about umbrella sampling through a nanotube

Dear GMXers, I'm trying to compute the PMF of a molecule along the centerline of a nanotube (the axial direction of the nanotube is parallel to the z axis). The nanotube is used as the reference group and the molecule as the pulling group. pull_geometry = position pull_dim= Y Y Y pull_s

[gmx-users] Including quadrupole-charge interaction in GROMACS

Dear GMXers, Is there a way in GROMACS to include quadrupole-charge interaction? Or is there a standard to way to mimic quadrupole moment using partial charge? Thank you. Best, Yanbin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please s

Re: [gmx-users] Including quadrupole-charge interaction in GROMACS

are implicit whenever you have a molecule withe > more than two partial charges. You don't have to include it explicitly. > There are, however, multipole expansion techniques to speed up > electrostatics calculations, but that's another story. > > Erik > > 15 jun 2011

[gmx-users] Representing bond coupling function form in a flexible water model

Dear GMXers, I'm trying to implementing a flexible water model in "Gordillo, M.C.; Marti, J. *J. Phys.: Condens. Matter* *2010*, *22*, 284111" using GROMACS. The intra-molecular water potential has the following form: V=D{[1-exp(-alpha*r1)]^2 + [1-exp(-alpha*r1)]^2} + k_a /2 *r3^2 + k_a*r3*(r1+r2

[gmx-users] Water Liquid-vapor interface: Negative surface tension by virial formula?

Dear GMXers, I'm computing the liquid-vapor surface tension for SPC/E water using GROMACS 4.5.3. The initial water box dimension is 3nm*3nm*3nm, containing 1807 water molecules, which is extended in z direction to a length of 12nm, to create two liquid-vapor interfaces. The ensemble is NVT. The sy

[gmx-users] Problem with computing graphite-water surface tension

Dear GMXers, I'm trying to compute the surface tension between water and graphite surface, using the C-O interaction parameters as in Werder et. al. J. Phys. Chem. B 2003. The expected contact angle, based on Young's equation, is 86 degrees (as reported in Werder's paper by droplet method). The SP

[gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group"

Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape. An error

Re: [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group

mposition cell of their charge group" > To: Discussion list for GROMACS users > Message-ID: <4cf73b92.40...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 2/12/2010 4:16 PM, WU Yanbin wrote: > > Dear GMXers, > > > > I

[gmx-users] g_tune_pme big standard deviation in perf.out output

Dear GMXers, I'm simulating a SPC/E water box with the size of 4nm by 4nm by 4nm. The command "g_tune_pme" was used to find the optimal PME node numbers, Coulomb cutoff radius and grid spacing size. The following command is used: g_tune_pme -np 24 -steps 5000 -resetstep 500 ... rcoul=1.5nm, rvdw=

[gmx-users] Center of mass motion removal for partial filled PBC box

Dear GMXers, I would like to reproduce the water droplet contact angle on graphite surface, as in Werder, T.; Walther, J. H.; Halicioglu, T.; Koumoutsakos, P. *J. Phys. Chem. B* *2003*, *107*, 1345-1352. The box size is 20nm by 20nm by 30nm. Graphite is represented by a two-layer carbon sheet. Af

[gmx-users] About "Apply Multiple bonded interactions" for dihedral potential definition

Hi, all, According to Manual v3.3, "It's possible to apply multiple bonded interactions of the same type on the same atoms" [12th line of Page 98]. If a dihedral potential for 4 neighboring atoms is defined 3 times using the "periodic type" in the topology file, like V=k1*(1+cos(phi-phi_s1)) V=k2*

[gmx-users] How to turn off Langevin thermostat for NVE Simulation

is calculated as mass/tau_t.) Does it influence my NVE simulation? Any method to turn the Langevin Dynamics off? Thanks. Yours Sincerely, WU Yanbin ___ gmx-users mailing listgmx-users

[gmx-users] Calculate individual force between each atom pair

advance. Yours Sincerely, WU Yanbin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] What molecule generator should be used if using GROMOS Force Field?

O does noe exist in GROMOS force field. And GROMOS manual can not be downloaded for free. Where can I find description for each atom type in GROMOS? Any suggestions? Thanks in advance. Yours Sincerely,

[gmx-users] Re: Calculate individual force between each atom pair

dvance. Yours Sincerely, WU Yanbin -- Message: 4 Date: Fri, 18 May 2007 09:14:22 +1000 From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Calculate individual force betwe

[gmx-users] Warning when using both LJ and Buckingham non-bonded interaction

is LJ (SR) Then is this topology OK? or I need other modifications? Thanks in advance. Yours Sincerely,

[gmx-users] Re: Warning when using both LJ and Buckingham non-bonded interaction

Hi, Everybody, And I found that if this simulation is on gromacs3.3, the warning becomes error. Yours Sincerely, WU Yanbin Message: 7 Date: Wed, 13 Jun 2007 21:35:42 -0500 From: "WU Yanbin" <[EMAIL PROTECTED]> Sub

[gmx-users] Re: Warning when using both LJ and Buckingham non-bonded interaction

Hi, David, Then it will be quite slow compared if I used the LJ or Buckingham function, right? Yours Sincerely, WU Yanbin -- Message: 6 Date: Thu, 14 Jun 2007 08:21:36 +0200 From: David van der Spoel

[gmx-users] Re: Warning when using both LJ and Buckingham non-bonded interaction

Hi, David, Then it will be quite slow using potential table compared if I used the LJ or Buckingham function, right? Yours Sincerely, WU Yanbin -- Message: 6 Date: Thu, 14 Jun 2007

[gmx-users] What if there are multi-definition of dihedrals?

. Yours Sincerely, WU Yanbin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Difference between pbc=full and pbc=xyz

Yours Sincerely, WU Yanbin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don&

[gmx-users] "check14" and "shuffle" options in grompp command

[ pairtypes ], the item in [ pairs ] would be removed? (2) "shuffle": Is it compulsory for parallel running? I read from the manual that it's a must. Thanks in advance. Yours Sincerely, WU Yanbin _

[gmx-users] How to change the box size during simuation

erely, WU Yanbin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don'

[gmx-users] How to generate GRO and TOP file for high-number-atom polymer?

Sincerely,   WU Yanbin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe reques

[gmx-users] What if the atom number exceed 99999 for Gromacs file?

;mdrun"? Thanks.     Yours Sincerely,