Re: [gmx-users] Regarding Glycine structure

[Justin Lemkul]

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,  for status/groups, 'help' for help)

0

Selection '0' parsed

cntrl+d

Last frame   1000 time 1.000
Analyzed 1001 frames, last time 1.000

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





   Sent with Mailtrack


On Tue, Mar 28, 2017 at 2:10 AM, Justin Lemkul  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,  for status/groups, 'help' for help)


0


Selection '0' parsed


cntrl+d


Last frame   1000 time 1.000
Analyzed 1001 frames, last time 1.000

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






   Sent with Mailtrack


On Mon, Mar 27, 2017 at 10:27 PM, Justin Lemkul  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 

Re: [gmx-users] Regarding Glycine structure

[Dilip H N]

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,  for status/groups, 'help' for help)
> 0
Selection '0' parsed
>cntrl+d
Last frame   1000 time 1.000
Analyzed 1001 frames, last time 1.000

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...??




   Sent with Mailtrack


On Tue, Mar 28, 2017 at 2:10 AM, Justin Lemkul  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,  for status/groups, 'help' for help)
>>
>>> 0
>>>
>> Selection '0' parsed
>>
>>> cntrl+d
>>>
>> Last frame   1000 time 1.000
>> Analyzed 1001 frames, last time 1.000
>>
>> 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
>
>
>>
>>
>>
>>    Sent with Mailtrack
>> > ral=cy16f01.di...@nitk.edu.in=22>
>>
>> On Mon, Mar 27, 2017 at 10:27 PM, Justin Lemkul  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

Re: [gmx-users] Regarding Glycine structure

[Justin Lemkul]

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,  for status/groups, 'help' for help)

0

Selection '0' parsed

cntrl+d

Last frame   1000 time 1.000
Analyzed 1001 frames, last time 1.000

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






   Sent with Mailtrack


On Mon, Mar 27, 2017 at 10:27 PM, Justin Lemkul  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



   Sent with Mailtrack



On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul  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

jalem...@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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.







--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral 

Re: [gmx-users] Regarding Glycine structure

[Dilip H N]

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,  for status/groups, 'help' for help)
> 0
Selection '0' parsed
>cntrl+d
Last frame   1000 time 1.000
Analyzed 1001 frames, last time 1.000

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..??





   Sent with Mailtrack


On Mon, Mar 27, 2017 at 10:27 PM, Justin Lemkul  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
>
>
>>    Sent with Mailtrack
>> > ral=cy16f01.di...@nitk.edu.in=22>
>>
>>
>> On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul  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
>>>
>>> jalem...@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
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow

Re: [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



   Sent with Mailtrack


On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul  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

jalem...@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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@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

jalem...@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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Regarding Glycine structure

[Dilip H N]

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..??
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...

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


   Sent with Mailtrack


On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul  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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] Regarding Glycine structure

[Justin Lemkul]

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Regarding Glycine structure

[Dilip H N]

I want the glycine to be in its non zwitter ionic form [NH2CH2COOH] as
such..



   Sent with Mailtrack


On Thu, Mar 23, 2017 at 11:35 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..??
>
> --
> With Best Regards,
>
> DILIP.H.N
> Research Scholar,
> Department of Chemistry, NITK.
>
>
>
>    Sent with Mailtrack
> 
>



-- 
With Best Regards,

DILIP.H.N
Research Scholar,
Department of Chemistry, NITK.
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