[gmx-users] How to examine our created topology

Faezeh Pousaneh fpoosaneh at gmail.com
Fri Feb 20 15:22:07 CET 2015

Thank you Justin for the helpful answer.

''This suggests the hydration free energy is wrong.'',
well I cann't say that, at least I see that the lower critical point of
water+lutidine mixture has big shift from the experimental one.

Best regards

On Fri, Feb 20, 2015 at 2:56 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 2/20/15 8:14 AM, Faezeh Pousaneh wrote:
>> Dear Justin
>> I have had asked you a question recently ''[gmx-users] How to examine our
>> created topology
>> <https://www.mail-archive.com/gromacs.org_gmx-users@
>> maillist.sys.kth.se/msg09758.html>''.
>> and you helped me with giving ABT structure of the molecule I am studding,
>> lutiidne.
>>   late reply, but I was checking the given topology in ATB. I am afraid it
>> does not produce expected behavior in water solution. One for example; it
>> is known that they mix at room temperature, but the given structure demix.
> This suggests the hydration free energy is wrong.
>  That is the problem I also have in my own created topology. It is
>> difficult
>> for me to get agreement with experiment for bulk lutidine, and its aqueous
>> solution at the same time.
>> Following this point, I would like to ask a general question ;
>> In order to study a binary mixture, for example lutidine and water here,
>> should I choose the charge distribution of lutidine (which I get from
>> quantum chemistry) from lutidine surrounded by lutidine, or lutidine
>> surrounded by water? that makes difference result in properties of bulk
>> lutidne and water lutidine mixture.
> The practical problem with the Gromos force fields is their empirical
> nature. The relationship to QM (unlike force fields like AMBER and CHARMM)
> is loose, at best.  Empirical fitting is done against condensed phase
> observables - density of neat liquid, the structure of that liquid,
> hydration free energy in various solvents, etc.  Obtaining those
> experimental data for targeting can be challenging, but that's what you
> need to use.  You can get an initial guess of the charge distribution from
> QM, but you won't necessarily wind up with anything like that when the
> parametrization is done.  Given that Gromos force fields are UA, there's
> little room for adjusting charges; most carbon groups have fixed properties
> (e.g. zero charge for alkyl substituents, etc) so you lose some flexibility.
> It may be wiser to simply use a different force field if the present
> choice doesn't work or requires too much effort.
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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