On 2/25/18 9:26 AM, Mahsa wrote:
Dear Mark,
Thank you for your reply. However, this is not clear for me yet since I
read this in the tutorial from Justin:
"There are two very important factors to evaluate and determine if EM was
successful. The first is the potential energy (printed at the end of the EM
process, even without -v). Epot should be negative. The second important
feature is the maximum force, Fmax, the target for which was set in
minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater than
1000 kJ mol-1 nm-1."
So I don't know whether it is correct to continue a simulation which gives
positive potential energy after the energy minimisation or not?
And also as I mentioned in my first post (the two different mdp files), I
don't know if I should consider pbc or not, in my simulation.
Unfortunately, I didn't understand your answer to my previous questions. Do
you mean that the steep integrator is not good to do energy minimization
for this type of simulation?
Would you please help me to fix these problems?
There is no problem. You're just comparing apples and oranges.
The tutorial system is a simple protein solvated by lots of water. The
potential energy function is the sum of bonded and nonbonded terms. In
an aqueous protein system, the nonbonded terms (particularly water-water
electrostatics) dominate the potential energy via favorable hydrogen
bond interactions. The internal (bonded) parameters for all the other
species are small in magnitude, by comparison, so the nonbonded terms
dominate and you get a negative potential energy.
In your case, you have comparatively weak nonbonded terms and larger
bonded terms, such that the potential energy function is dominated by
internal energy, which is by definition, positive.
This is not an indication that anything is wrong with the algorithms used.
-Justin
Regards,
Mahsa
On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
Hi,
Even if there are minima on the surface that have negative energy (which
will depend how the model was developed, which you should look into)
there's no reason to expect an arbitrary starting configuration will find
one after a steepest descent search. A tangled pile of strings will stay
tangled.
Mark
On Fri, Feb 23, 2018, 23:28 Mahsa E <ebadi.ma...@gmail.com> wrote:
Hello,
I want to simulate a box of polymer (32 chains) with salt. I started with
one chain of the polymer in the box. However, after the energy
minimisation, the energy is still positive. I found the discussion in the
link below very similar to the problem I have:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
/2017-February/111219.html
and tried the tips from Justin in the link but I still get positive
energy.
This is my first MDP file:
define =
integrator = steep
nsteps = -1
nstcgsteep = 10
constraints = none
lincs_order = 8
emtol = 20
emstep = 0.01
comm-mode = Linear
nstcomm = 1
nstcalcenergy = 1
; Output frequency for energies to log file and energy file
nstlog = 1
nstenergy = 1
ns_type = grid
cutoff-scheme = verlet
coulombtype = PME
nstlist = 10
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 1
pbc = xyz
and this is the second one which I tried to follow the tips from the link
mentioned above:
define =
integrator = steep
nsteps = -1
nstcgsteep = 10
constraints = none
lincs_order = 8
emtol = 20
emstep = 0.01
comm-mode = Linear
nstcomm = 1
nstcalcenergy = 1
; Output frequency for energies to log file and energy file
nstlog = 1
nstenergy = 1
ns_type = grid
cutoff-scheme = group
coulombtype = cut-off
nstlist = 0
rlist = 0
rcoulomb = 0
rvdw = 0
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 1
pbc = no
My questions are:
- I'm not sure if either of these MDP files are correct for the system
I'm
trying to simulate?
- Why energy is positive in this simulation? Is there something
fundamentally wrong in the simulation which I'm not aware of?
Regards,
Mahsa
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