Re: [gmx-users] Dimer simulation problem

2011-09-26 Thread Kavyashree M 
Hello,

Yes i did that. but qualitatively i did not see any such clashes.
But i do not know how to quantify it by calculations.

Thank you
with regards
Kavya
On Mon, Sep 26, 2011 at 5:51 PM, Sarath Chandra Dantu wrote:

>
> > Hello again,
> >
> > I centered it and then did the calculation again for minimum image
> > distance
> > but still it showed the same graph as without centering. I tried
> > visualising
> > it
> > using vmd but could not see any such clashes. since I am new to vmd
> > I do not know whether it is possible to calculate such clashes if at all
> > in vmd? I am using dodecahedron box. can it be visualised as it is in
> vmd?
> >
>
> In VMD go to graphics then representations and select periodic. In
> periodic by clicking on +/- of each axis you can check if your protein
> bumps into itself.
>
> Best,
>
> Sarath
>
> > Thank you
> > With regards
> > Kavya
> >
> > On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M  wrote:
> >
> >> Thanks.
> >>
> >>
> >> On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul 
> >> wrote:
> >>
> >>>
> >>>
> >>> Kavyashree M wrote:
> >>>
>  Dear users,
> 
>  I was trying to simulate a protein dimer covalently bond with
>  a disulphide bond (230+230 aa long). I used usual protocol
>  as used for simulation of a monomeric protein, using gromacs-
>  4.5.3, dodecahedron box, tip4p water model and protein to
>  box distance of 1 (-d in editconf). In the middle of the simulation
>  when i checked for minimum image violation there was huge
>  clashes. I am extremely sorry I have been asking regarding this
>  many times but in this it is a dimer and I am not sure what mistake
>  I have done because this happened while simulating another dimer
>  also though not sever. Hence I seek some guidance from this
>  community regarding the problem. I attach the graph herewith.
>  Kindly help. Let me know if I need to give any other information.
> 
> 
> >>> Please see my post from yesterday for a more detailed reply to this
> >>> exact
> >>> same type of question.  I am beginning to suspect there's a problem
> >>> with
> >>> g_mindist, but I have no solid evidence for that claim, just a hunch.
> >>> It
> >>> looks like your protein crosses a periodic boundary and that messes up
> >>> the
> >>> calculation.  Please center the protein in the box with trjconv -center
> >>> and
> >>> re-analyze to see if there are any differences.
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==**==
> >>>
> >>> Justin A. Lemkul
> >>> Ph.D. Candidate
> >>> ICTAS Doctoral Scholar
> >>> MILES-IGERT Trainee
> >>> Department of Biochemistry
> >>> Virginia Tech
> >>> Blacksburg, VA
> >>> jalemkul[at]vt.edu | (540) 231-9080
> >>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>>
> >>> ==**==
> >>> --
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >>> Please search the archive at http://www.gromacs.org/**
> >>> Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before
> >>> posting!
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> >>> Can't post? Read
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> http://www.gromacs.org/Support/Mailing_Lists>
> >>>
> >>
> >>
> > --
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>
>
> 
> Sarath Chandra Dantu
> Computational Biomolecular Chemistry
> Max Planck Institute of Biophysical Chemistry
> Am Fassberg 11,
> Gottingen
> 37077
> Germany
>
> Email: dsar...@gwdg.de
> Tel: ++49-551-201-2320
> Fax: ++49-551-201-2302
>
>
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Re: [gmx-users] Dimer simulation problem

2011-09-26 Thread Sarath Chandra Dantu 

> Hello again,
>
> I centered it and then did the calculation again for minimum image
> distance
> but still it showed the same graph as without centering. I tried
> visualising
> it
> using vmd but could not see any such clashes. since I am new to vmd
> I do not know whether it is possible to calculate such clashes if at all
> in vmd? I am using dodecahedron box. can it be visualised as it is in vmd?
>

In VMD go to graphics then representations and select periodic. In
periodic by clicking on +/- of each axis you can check if your protein
bumps into itself.

Best,

Sarath

> Thank you
> With regards
> Kavya
>
> On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M  wrote:
>
>> Thanks.
>>
>>
>> On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul 
>> wrote:
>>
>>>
>>>
>>> Kavyashree M wrote:
>>>
 Dear users,

 I was trying to simulate a protein dimer covalently bond with
 a disulphide bond (230+230 aa long). I used usual protocol
 as used for simulation of a monomeric protein, using gromacs-
 4.5.3, dodecahedron box, tip4p water model and protein to
 box distance of 1 (-d in editconf). In the middle of the simulation
 when i checked for minimum image violation there was huge
 clashes. I am extremely sorry I have been asking regarding this
 many times but in this it is a dimer and I am not sure what mistake
 I have done because this happened while simulating another dimer
 also though not sever. Hence I seek some guidance from this
 community regarding the problem. I attach the graph herewith.
 Kindly help. Let me know if I need to give any other information.


>>> Please see my post from yesterday for a more detailed reply to this
>>> exact
>>> same type of question.  I am beginning to suspect there's a problem
>>> with
>>> g_mindist, but I have no solid evidence for that claim, just a hunch.
>>> It
>>> looks like your protein crosses a periodic boundary and that messes up
>>> the
>>> calculation.  Please center the protein in the box with trjconv -center
>>> and
>>> re-analyze to see if there are any differences.
>>>
>>> -Justin
>>>
>>> --
>>> ==**==
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>>>
>>> ==**==
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Searchbefore
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read
>>> http://www.gromacs.org/**Support/Mailing_Lists
>>>
>>
>>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Sarath Chandra Dantu
Computational Biomolecular Chemistry
Max Planck Institute of Biophysical Chemistry
Am Fassberg 11,
Gottingen
37077
Germany

Email: dsar...@gwdg.de
Tel: ++49-551-201-2320
Fax: ++49-551-201-2302


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Re: [gmx-users] Dimer simulation problem

2011-09-26 Thread Mark Abraham 

On 26/09/2011 10:02 PM, Kavyashree M wrote:

Hello again,

I centered it and then did the calculation again for minimum image 
distance
but still it showed the same graph as without centering. 


Have you followed the kind of workflow suggested here? 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions



I tried visualising it
using vmd but could not see any such clashes. since I am new to vmd
I do not know whether it is possible to calculate such clashes if at all
in vmd? I am using dodecahedron box. can it be visualised as it is in vmd?


Yes, one can be visualized, but some preparation with trjconv -ur 
compact (as hinted at in trjconv -h) is a good idea.


Mark



Thank you
With regards
Kavya

On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M > wrote:


Thanks.


On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



Kavyashree M wrote:

Dear users,

I was trying to simulate a protein dimer covalently bond with
a disulphide bond (230+230 aa long). I used usual protocol
as used for simulation of a monomeric protein, using gromacs-
4.5.3, dodecahedron box, tip4p water model and protein to
box distance of 1 (-d in editconf). In the middle of the
simulation
when i checked for minimum image violation there was huge
clashes. I am extremely sorry I have been asking regarding
this
many times but in this it is a dimer and I am not sure
what mistake
I have done because this happened while simulating another
dimer
also though not sever. Hence I seek some guidance from this
community regarding the problem. I attach the graph herewith.
Kindly help. Let me know if I need to give any other
information.


Please see my post from yesterday for a more detailed reply to
this exact same type of question.  I am beginning to suspect
there's a problem with g_mindist, but I have no solid evidence
for that claim, just a hunch.  It looks like your protein
crosses a periodic boundary and that messes up the
calculation.  Please center the protein in the box with
trjconv -center and re-analyze to see if there are any
differences.

-Justin

-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- 
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Re: [gmx-users] Dimer simulation problem

2011-09-26 Thread Kavyashree M 
Hello again,

I centered it and then did the calculation again for minimum image distance
but still it showed the same graph as without centering. I tried visualising
it
using vmd but could not see any such clashes. since I am new to vmd
I do not know whether it is possible to calculate such clashes if at all
in vmd? I am using dodecahedron box. can it be visualised as it is in vmd?

Thank you
With regards
Kavya

On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M  wrote:

> Thanks.
>
>
> On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> Kavyashree M wrote:
>>
>>> Dear users,
>>>
>>> I was trying to simulate a protein dimer covalently bond with
>>> a disulphide bond (230+230 aa long). I used usual protocol
>>> as used for simulation of a monomeric protein, using gromacs-
>>> 4.5.3, dodecahedron box, tip4p water model and protein to
>>> box distance of 1 (-d in editconf). In the middle of the simulation
>>> when i checked for minimum image violation there was huge
>>> clashes. I am extremely sorry I have been asking regarding this
>>> many times but in this it is a dimer and I am not sure what mistake
>>> I have done because this happened while simulating another dimer
>>> also though not sever. Hence I seek some guidance from this
>>> community regarding the problem. I attach the graph herewith.
>>> Kindly help. Let me know if I need to give any other information.
>>>
>>>
>> Please see my post from yesterday for a more detailed reply to this exact
>> same type of question.  I am beginning to suspect there's a problem with
>> g_mindist, but I have no solid evidence for that claim, just a hunch.  It
>> looks like your protein crosses a periodic boundary and that messes up the
>> calculation.  Please center the protein in the box with trjconv -center and
>> re-analyze to see if there are any differences.
>>
>> -Justin
>>
>> --
>> ==**==
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>>
>> ==**==
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>
>
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Re: [gmx-users] Dimer simulation problem

2011-09-21 Thread Kavyashree M 
Thanks.

On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> Dear users,
>>
>> I was trying to simulate a protein dimer covalently bond with
>> a disulphide bond (230+230 aa long). I used usual protocol
>> as used for simulation of a monomeric protein, using gromacs-
>> 4.5.3, dodecahedron box, tip4p water model and protein to
>> box distance of 1 (-d in editconf). In the middle of the simulation
>> when i checked for minimum image violation there was huge
>> clashes. I am extremely sorry I have been asking regarding this
>> many times but in this it is a dimer and I am not sure what mistake
>> I have done because this happened while simulating another dimer
>> also though not sever. Hence I seek some guidance from this
>> community regarding the problem. I attach the graph herewith.
>> Kindly help. Let me know if I need to give any other information.
>>
>>
> Please see my post from yesterday for a more detailed reply to this exact
> same type of question.  I am beginning to suspect there's a problem with
> g_mindist, but I have no solid evidence for that claim, just a hunch.  It
> looks like your protein crosses a periodic boundary and that messes up the
> calculation.  Please center the protein in the box with trjconv -center and
> re-analyze to see if there are any differences.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
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Re: [gmx-users] Dimer simulation problem

2011-09-21 Thread Justin A. Lemkul 



Kavyashree M wrote:

Dear users,

I was trying to simulate a protein dimer covalently bond with
a disulphide bond (230+230 aa long). I used usual protocol
as used for simulation of a monomeric protein, using gromacs-
4.5.3, dodecahedron box, tip4p water model and protein to
box distance of 1 (-d in editconf). In the middle of the simulation
when i checked for minimum image violation there was huge
clashes. I am extremely sorry I have been asking regarding this
many times but in this it is a dimer and I am not sure what mistake
I have done because this happened while simulating another dimer
also though not sever. Hence I seek some guidance from this
community regarding the problem. I attach the graph herewith.
Kindly help. Let me know if I need to give any other information.



Please see my post from yesterday for a more detailed reply to this exact same 
type of question.  I am beginning to suspect there's a problem with g_mindist, 
but I have no solid evidence for that claim, just a hunch.  It looks like your 
protein crosses a periodic boundary and that messes up the calculation.  Please 
center the protein in the box with trjconv -center and re-analyze to see if 
there are any differences.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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[gmx-users] Dimer simulation problem

2011-09-21 Thread Kavyashree M 
Dear users,

I was trying to simulate a protein dimer covalently bond with
a disulphide bond (230+230 aa long). I used usual protocol
as used for simulation of a monomeric protein, using gromacs-
4.5.3, dodecahedron box, tip4p water model and protein to
box distance of 1 (-d in editconf). In the middle of the simulation
when i checked for minimum image violation there was huge
clashes. I am extremely sorry I have been asking regarding this
many times but in this it is a dimer and I am not sure what mistake
I have done because this happened while simulating another dimer
also though not sever. Hence I seek some guidance from this
community regarding the problem. I attach the graph herewith.
Kindly help. Let me know if I need to give any other information.

Thanking you
With Regards
M. Kavyashree
[image: therm.png]
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