[gmx-users] Positive potential energy
Mahsa
ebadi.mahsa at gmail.com
Sun Feb 25 16:16:24 CET 2018
Dear Justin,
Thank you for your reply!
In general, is it a good approach to first use steep algorithm for EM and
then to further minimize do EM with cg algorithm, on the output structure?
Could you please comment on my question about the mdp files and pbc as
well? Actually, you mentioned here:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
/2017-February/111219.html
that for one chain of polymer in vacuum, pbc should not be considered. So,
for my simulation, in the first step I have one chain in vaccum and
eventually I want to pack the whole box with polymer chains and ions,
should I use pbc or not and which of the mdp files in my first post is
correct?
Regards,
Mahsa
On Sun, Feb 25, 2018 at 3:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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.abraham at 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.mahsa at 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
>>>> --
>>>> 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/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>> --
>>> 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/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
> --
> 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/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list