[gmx-users] emtol criterion

[Justin Lemkul]

On 11/28/19 1:50 AM, Kevin Boyd wrote:
>> For GROMACS, I think the emtol
>> value should be reported, but this varies by personal preference in most
>> papers, unfortunately.
> I had thought that emtol had no particular significance for minimizations
> used to set up typical MD simulations, as long as the system was
> sufficiently minimized as to not explode. Is there any evidence that stable
> simulated systems behave differently based on the minimum energy they
> achieved during minimization?

I have not seen such a comparison for "normal" MD simulations, though 
for calculations like NMA, one needs to achieve a very low force before 
proceeding.

-Justin

> On Wed, Nov 27, 2019 at 4:05 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 11/27/19 12:39 PM, Christos Deligkaris wrote:
>>> dear all,
>>>
>>> I am trying to decide on a reasonable cutoff for emtol.
>>>
>>> The Gromacs manual (section 3.10 on energy minimization) states that a
>>> reasonable criterion for emtol can be found from the rms force a harmonic
>>> oscillator would exhibit at room temperature (Equation 3.125). For a weak
>>> oscillator (100 cm^-1) a force of 7.7 kJ/mol/nm is obtained. This number
>> is
>>> consistent with the default criterion of 10.0 kJ/nm/mol. It is not clear
>> to
>>> me how the value of 100cm^-1 was chosen in this example though.
>> I can't comment directly on this aspect, but a value of 100 cm^-1 is
>> about 10x lower than most bond vibrations in biological systems, so this
>> would correspond to some slower, low-amplitude motion in, e.g. a
>> protein. So in essence, the back-of-the-envelope math suggests forces
>> converging below this value would put you at an energy minimum with only
>> very low-frequency modes. In practice, this is a very strict criterion
>> and often difficult to achieve in mixed precision (and sometimes even in
>> double).
>>
>>> Using a frequency of 1900cm^-1 and 7 amu reduced mass for CO stretching I
>>> got 122 kJ/mol/nm which appears to be more consistent with the criterion
>> of
>>> 1000 kJ/nm/mol used in the lysozyme tutorial:
>>> http://www.mdtutorials.com/gmx/lysozyme/05_EM.html
>>>
>>> In the literature I see the number of minimization steps (nsteps)
>> reported
>>> but not a specific criterion.
>> In my experience, this generally varies by either (1) software or (2)
>> the precision with which the authors report their settings. You can say
>> that there were "5000 steps of steepest descent minimization" in
>> GROMACS, but more often than not, that's what is set as nsteps but not
>> actually used. Other software (CHARMM, AMBER, etc) will gladly perform
>> exactly as many steps of SD as you tell it to rather than bailing out
>> after a convergence criterion is reached. For GROMACS, I think the emtol
>> value should be reported, but this varies by personal preference in most
>> papers, unfortunately.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> 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
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================