[gmx-users] Regarding Glycine structure
Justin Lemkul
jalemkul at vt.edu
Tue Mar 28 13:58:05 CEST 2017
On 3/27/17 11:34 PM, Dilip H N wrote:
> 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...??
>
By making two groups instead of one. That's what an RDF tells you - how the
atoms in group X are distributed around the atoms in group Y. The typo is
insignificant because now we're just talking about N-terminal protons instead of
alpha H atoms. My previous points stand.
-Justin
>
>
>
> <https://mailtrack.io/> Sent with Mailtrack
> <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22>
>
> 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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>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>> ==================================================
>>>>
>>>> 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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>>>>
>>>
>>>
>>>
>> --
>> ==================================================
>>
>> 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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>> 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
==================================================
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