[gmx-users] How to examine our created topology

Faezeh Pousaneh fpoosaneh at gmail.com
Sun Feb 15 15:39:47 CET 2015

Dear Justin,

I simulate 2,6 dimethylpyridine (lutidine), C7H9N. I use ''gromos43a1''
force field, and I have taken the charges on atoms from Gaussian software.
By manipulating charges on the atoms I can get better agreement with
experiment for the bulk, but then I loose it's aqueous properties (mixture
of water-lutidine). How to overcome this problem?
Actually your suggestion ''but the relative contributions of these terms
depend on the chemical nature of the molecule(s) involved'' is not clear
for me.

Best regards
Faezeh Pousaneh
Department of Theoretical Physics
KTH Royal Institute of Technology
AlbaNova University Center
SE-106 91 Stockholm, Sweden

On Sun, Feb 15, 2015 at 2:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 2/14/15 5:21 AM, Faezeh Pousaneh wrote:
>> Dear expert,
>> I have created topology for an unstudied (simulation) molecule, and I can
>> run it successfully.
>> 1- How many or which quantities at least must be checked with experiment
>> to
>> become sure of the created topology? and if we find some difference with
>> experiment, to what percent this differences can be acceptable? (for
>> instance, if the experimental value of the density is 920 kg/m^3, is 1000
>> kg/m^3 OK?).
> That's a fairly large difference.  Typically agreement for bulk properties
> like these is 1-2% deviation for "good" force fields.
>  2- If we intend to improve the differences with the experimental values,
>> what are the best ways? is changing slightly the charges on the atoms can
>> be a good way (let us say we correctly have defined bonds, angels, ect
>> according to the force filed)?
> The real answer comes from what the force field parametrization protocol
> should be.  What force field are you using?  What did the developers do to
> parametrize the existing compounds in the force field?  For obtaining
> correct condensed phase properties, charges and LJ parameters are often
> tuned, but the relative contributions of these terms depend on the chemical
> nature of the molecule(s) involved.
> -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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