[gmx-users] Regarding Glycine structure

[Justin Lemkul]

On 3/27/17 8:50 AM, Dilip H N wrote:
> Thanks Justin,
>
> But my doubts are..
> 1] after energy minimization of both glycine non zwitterionic form and
> zwitterionic form with water, if i visualize it in vmd, the bond between
> some of the water molecules are broken.. why is this so..??

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

What you see on the VMD display is its best guess as to how things are 
connected.  That's not always right.  The topology is always right.  That's why 
trjconv exists.

> 2] and ran nvt,npt,md simulations respectively...and during analysis part i
> am getting only similar two types of RDF graphs...why is this happening...i
> have made all the indexing, etc., proper...
>

You have provided no useful information about what these RDF plots are or how 
you acquired them, so there's no point for either of us in guessing.  Maybe the 
distribution(s) that you're looking at simply don't vary as a function of 
protonation state.

> Is there any tutorials for these as an example..?? solving this would help
> me a lot....
>

It's an amino acid in water; it's as easy of a protein system as there is. 
There's nothing special about it that requires a tutorial.

-Justin

>
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>
> On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/23/17 2:05 PM, Dilip H N wrote:
>>
>>> Hello,
>>>
>>> I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and in
>>> the first step if i do the energy minimization and then visualizes the
>>> mixture, the glycine is no more in its pure form as before instead it has
>>> been converted to its zwitter ionic form [NH3CH2COO], and some Hydrogen
>>> bonds with water are also broken. How can i solve these both issues..??
>>>
>>>
>> Glycine didn't convert between forms.  That's impossible; bonds can't
>> break or form in a molecular mechanical process.  The termini are exactly
>> what you assigned them to be.  If you want them to be something else, you
>> have to assign them as such with pdb2gmx.  Though you should note that NH2
>> and COOH can't coincide at any real pH value.
>>
>> -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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>
>
>

-- 
==================================================

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

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