[gmx-users] distance dependent energy

[Cuong Nguyen]

Hi Mark,

I manage to find the way to record the energy but have not figured it out
yet. I used the .mdp file as below:

title                    = Molecular dynamics simulation at 298K
cpp                      = cpp
integrator               = md
dt                       = 0.001
nsteps                   = 20000000 ; 20 ns
comm-mode                = Linear
nstcomm                  = 200
nstxout                  = 2000 ;trajectory file
nstvout                  = 2000 ; velocity file
nstfout                  = 0
nstlog                   = 300 ;log file
nstenergy                = 300 ; energy file
nstxtcout                = 300
nstlist                  = 100
ns_type                  = grid
pbc                      = xyz
coulombtype              = pme
rlist                    = 1.3
rcoulomb                 = 1.3
vdw-type                 = Cut-off
rvdw                     = 1.3
Tcoupl                   = Nose-Hoover; Berendsen ; no pcoupl = NVT?
nsttcouple               = 50; half nstlist
tc_grps                  = System
tau_t                    = 2.0
ref_t                    = 298.15
gen_vel                  = no
gen_seed                 = 94839
constraints              = All-bonds
constraint-algorithm     = lincs

Do you have any links or tutorials for that?

Best regards,

Van



Cuong Van Nguyen (PhD Student)
Department of Chemical Engineering
Curtin University, Western Australia
Tel. (+61) 45 221 3981


On 2 October 2015 at 11:16, Cuong Nguyen <nvcuong68 at gmail.com> wrote:

> Thank you Mark and Erik,
> Van
>
>
> On Wednesday, 23 September 2015, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> On Tue, Sep 22, 2015 at 5:47 PM Cuong Nguyen <nvcuong68 at gmail.com> wrote:
>>
>> > Dear Gromacs users,
>> >
>> > I would like to work out the energy (total and kinetic) as a function of
>> > the distance from the center of mass of a droplet. However, using
>> g_energy
>> > just gave me the values as a function of time. Could anyone tell me the
>> way
>> > to get the distance dependent values?
>> >
>>
>> First, you'd have to record them. mdrun doesn't work by first evaluating a
>> giant matrix of per-anything energies, and then adding them up. You can
>> use
>> energy groups to break down the short-ranged non-bonded component of the
>> potential energy into intra- and inter-group terms, but you can only have
>> 256 of them, and only with the group scheme, and only if you're not
>> concerned about diffusion (or are prepared to use dynamic selections and
>> mdrun -rerun creatively). And the work you have to put in to get that out
>> is not really worth thinking about unless you know exactly what you're
>> going to learn from the result.
>>
>> Mark
>> --
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>
>
> --
>
>
> Cuong Van Nguyen (PhD Student)
> Department of Chemical Engineering
> Curtin University, Western Australia
> Tel. (+61) 45 221 3981
>
>
>