[gmx-users] Positive potential energy
Mahsa
ebadi.mahsa at gmail.com
Mon Feb 26 09:49:57 CET 2018
Hi,
Thanks for your help, Justin!
Regards,
Mahsa
On Sun, Feb 25, 2018 at 5:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/25/18 10:15 AM, Mahsa wrote:
>
>> 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?
>>
>
> I usually don't find multiple steps of EM needed in most cases, but
> occasionally. The purpose of EM is to find a plausible starting point for
> the simulation - you can never know if you're in the global minimum so it's
> a bit of working in the dark, anyway. But the gradient (max force) reports
> on that.
>
> 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?
>>
>
> If you're working in the condensed phase, you need finite cutoffs, PME,
> and PBC.
>
> -Justin
>
>
> 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
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>>>>>> posting!
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>>>>>> --
>>>>>>
>>>>> Gromacs Users mailing list
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>>>>>
>>>>> --
>>> ==================================================
>>>
>>> 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
>>>
>>> ==================================================
>>>
>>>
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>>>
> --
> ==================================================
>
> 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
>
> ==================================================
>
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> Gromacs Users mailing list
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