[gmx-users] Regarding Glycine structure

Tue Mar 28 05:34:36 CEST 2017

Sorry it was a typing mistake..it is actually

1] To make indexes:-
gmx make_ndx -f md.gro -o Hn-OW.ndx

> del 2
Removed group 2 'SOL'
 > del 1
Removed group 1 'Water'
 > del 0
Removed group 0 'System'
> a H1 H2 H3 OW
Found xxx atoms with name H1 H2 H3 OW
0 H1 H2 H3 OW : xxx atoms
> q

2]Then, Using the index to calculate the pair correlation function for all
frames:-
gmx rdf -f md.trr -s md.tpr -n Hn-OW.ndx -o rdf_Hn-OW.xvg

Available static index groups:
 Group  0 "H1_H2_H3 OW" (xxx atoms)
Specify a selection for option 'ref'
(Reference selection for RDF computation):
(one per line, <enter> for status/groups, 'help' for help)
> 0
Selection '0' parsed
>cntrl+d
Last frame       1000 time 10000.000
Analyzed 1001 frames, last time 10000.000

3] View the plot:

xmgrace rdf_Hn-OW.xvg

and if i view the obtained graphs in xmgrace i am getting only two kinds of
graphs...ie.,
(a) for Hn-OW,Ha-OW etc, graphs are same for OW end indexing and
(b) for Hn-HW,Ha-HW etc., graphs are same for HW end indexing..

My doubts are..
1)What is this only two kinds of graphs am i getting..?? ,
2)I hope the above procedure to get RDF ie., commands 1] gmx make_ndx.....,
2] gmx rdf ..... 3] xmgrace..... are correct in accordance..
3)Or is there any mistake that i am doing..?? Can anybody rectify my
mistakes if any..??

as you have told how to put  Hn atoms in one group and the Ow in
another...??

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On Tue, Mar 28, 2017 at 2:10 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/27/17 3:55 PM, Dilip H N wrote:
>
>> i want to calculate RDF of glycine  of Hn-OW, Hn-HW, Ha-OW, Ha-HW,  Ca-OW,
>>  etc.,
>> So my commands were as follows...
>>
>> 1] To make indexes:-
>> gmx make_ndx -f md.gro -o Hn-OW.ndx
>>
>> del 2
>>>
>> Removed group 2 'SOL'
>>  > del 1
>> Removed group 1 'Water'
>>  > del 0
>> Removed group 0 'System'
>>
>>> a H1 H2 H3 OW
>>>
>> Found xxx atoms with name H1 H2 H3 OW
>> 0 HA1_HA2_OW : xxx atoms
>>
>>> q
>>>
>>
>>
>> 2]Then, Using the index to calculate the pair correlation function for all
>> frames:-
>> gmx rdf -f md.trr -s md.tpr -n Hn-OW.ndx -o rdf_Hn-OW.xvg
>>
>> Available static index groups:
>>  Group  0 "HA1_HA2_OW" (xxx atoms)
>> Specify a selection for option 'ref'
>> (Reference selection for RDF computation):
>> (one per line, <enter> for status/groups, 'help' for help)
>>
>>> 0
>>>
>> Selection '0' parsed
>>
>>> cntrl+d
>>>
>> Last frame       1000 time 10000.000
>> Analyzed 1001 frames, last time 10000.000
>>
>> 3] View the plot:
>>
>> xmgrace rdf_Hn-OW.xvg
>>
>> and if i view the obtained graphs in xmgrace i am getting only two kinds
>> of
>> graphs...ie.,
>> (a) for Hn-OW,Ha-OW etc, graphs are same for OW end indexing and
>> (b) for Hn-HW,Ha-HW etc., graphs are same for HW end indexing..
>>
>> My doubts are..
>> 1)What is this only two kinds of graphs am i getting..?? ,
>> 2)I hope the above procedure to get RDF ie., commands 1] gmx
>> make_ndx.....,
>> 2] gmx rdf ..... 3] xmgrace..... are correct in accordance..
>> 3)Or is there any mistake that i am doing..?? Can anybody rectify my
>> mistakes if any..??
>>
>>
> You're probably just getting a bunch of garbage.  You're apparently
> merging the alpha hydrogen atoms and water oxygens into one group, which
> makes no sense at all.  If you want Ha-Ow RDF, then the Ha* atoms should be
> in one group and the Ow in another.
>
> -Justin
>
>
>>
>>
>>
>>   <https://mailtrack.io/> Sent with Mailtrack
>> <https://mailtrack.io/install?source=signature&lang=en&refer
>> ral=cy16f01.dilip at nitk.edu.in&idSignature=22>
>>
>> On Mon, Mar 27, 2017 at 10:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> 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
>>>
>>>
>>>   <https://mailtrack.io/> Sent with Mailtrack
>>>> <https://mailtrack.io/install?source=signature&lang=en&refer
>>>> ral=cy16f01.dilip at nitk.edu.in&idSignature=22>
>>>>
>>>>
>>>> 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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> 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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
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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
>
> ==================================================
> --
> 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
>
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student