Re: [gmx-users] Regarding centering the molecule/protein during Simulation

2017-05-29 Thread Peter Kroon 
Keep discussions on the list. I am not your personal help. I will not
respond to future e-mails to my personal address.


Type `gmx trjconv -h` and read.

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


On 29-05-17 13:43, Dilip H N wrote:
> Thank you...
> nw the amino-acid is placed in the middle, but i have two solvents as
> mixture (solvent A,B).
> But the problem is tht nw the amino-acid remains in the centre but the
> solvent B is moving out of the box
> How can i solve this issue..??
>
> Thank you...
>
> On Mon, May 29, 2017 at 4:10 PM, Peter Kroon  > wrote:
>
> Keep discussions on the list.
>
> As i wrote in my previous mail, you need `gmx trjconv -pbc mol -center
> ...`. In your example this would be:
>
> > gmx tjrconv -f md.xtc -s md.tpr -pbc mol -o mdx.xtc *-center*
>
> > vmd  mdx.xtc
>
> If you can't figure it out from here, try `gmx trjconv -h` and read.
>
> Peter
>
>
> On 29-05-17 12:16, Dilip H N wrote:
> > Thank you for reply..
> >
> > I have ran energy minimization,followed by nvt, followed by md run.
> > In this md run mdp (md.mdp),
> > nw after the simulation ends, i can view the trajectory by giving
> > command as :-
> >  gmx trjconv -f md.xtc -s md.tpr -pbc mol -o mdx.trr/xtc/gro
> >
> > and nw if i view the mdx.trr/xtc/gro in the vmd as :-
> >  vmd  mdx.trr/xtc/gro
> >
> > will the amino-acid only be at the centre while viewing it throught
> > the trajectory and moving solvent molecules around as usual..??
> >
> > Or can u kindly help me which r the exact commands tht i need to
> give
> > in order tht while viewing the full trajectory in vmd only the
> > amino-acid should be in centre , whereas the solvent molecules
> should
> > move around as usual..
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
> >    Sent with Mailtrack
> >
> 
>  
> >
> >
>
>
>
>
>
> -- 
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student


-- 
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 centering the molecule/protein during Simulation

2017-05-29 Thread Peter Kroon 
Keep discussions on the list.

As i wrote in my previous mail, you need `gmx trjconv -pbc mol -center
...`. In your example this would be:

> gmx tjrconv -f md.xtc -s md.tpr -pbc mol -o mdx.xtc *-center*

> vmd  mdx.xtc

If you can't figure it out from here, try `gmx trjconv -h` and read.

Peter


On 29-05-17 12:16, Dilip H N wrote:
> Thank you for reply..
>
> I have ran energy minimization,followed by nvt, followed by md run.
> In this md run mdp (md.mdp),
> nw after the simulation ends, i can view the trajectory by giving
> command as :-
>  gmx trjconv -f md.xtc -s md.tpr -pbc mol -o mdx.trr/xtc/gro
>  
> and nw if i view the mdx.trr/xtc/gro in the vmd as :-
>  vmd  mdx.trr/xtc/gro 
>
> will the amino-acid only be at the centre while viewing it throught
> the trajectory and moving solvent molecules around as usual..??
>
> Or can u kindly help me which r the exact commands tht i need to give
> in order tht while viewing the full trajectory in vmd only the
> amino-acid should be in centre , whereas the solvent molecules should
> move around as usual..
>
> -- 
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
> 
>


-- 
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 centering the molecule/protein during Simulation

2017-05-29 Thread Peter Kroon 
Hi,


I would not do this. I would run my simulation as normal (no position
restraints), and center my amino acid in post processing (gmx trjconv
-pbc mol -center ...). You may need to make an appropriate index file.
Alternatively you may want to use -fit instead of -center, but that's a
matter of taste.


Peter


On 29-05-17 08:16, Saumyak Mukherjee wrote:
> Hi Dilip,
>
> To fix the amino acid at the centre of the box first you have to use -c
> flag with editconf. Later, during simulation you have to use
> define=-dposres in the mdp file. This will include the position restrain
> defined in the posre.itp file generated during the use of pdb2gmx.
>
> Best,
> Saumyak
>
> On 29 May 2017 at 10:59, Dilip H N  wrote:
>
>> Hello,
>> I have ran a md simulation of a amino-acid with solvent mixture. Now i view
>> the trajectory in vmd and see tht the amino-acid moves sometimes toward the
>> edge of the box,sometimes towards the corners and so on...
>>  Now how can i centre only the amino-acid to the centre of the box and rest
>> (ie.,solvent mixture) to move as it is..ie., if i view the trajectory in
>> vmd i want to fix only the amino-acid to be in centre,whereas the solvent
>> mixtures to move around during the trajectory...
>> How can i do this,...??
>>
>> Thank you...
>>
>> --
>> With Best Regards,
>>
>> DILIP.H.N
>> Ph.D Student
>>
>>
>>
>>    Sent with Mailtrack
>> > referral=cy16f01.di...@nitk.edu.in=22>
>> --
>> 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.
>>
>
>


-- 
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 centering the molecule/protein during Simulation

2017-05-29 Thread Saumyak Mukherjee 
Hi Dilip,

To fix the amino acid at the centre of the box first you have to use -c
flag with editconf. Later, during simulation you have to use
define=-dposres in the mdp file. This will include the position restrain
defined in the posre.itp file generated during the use of pdb2gmx.

Best,
Saumyak

On 29 May 2017 at 10:59, Dilip H N  wrote:

> Hello,
> I have ran a md simulation of a amino-acid with solvent mixture. Now i view
> the trajectory in vmd and see tht the amino-acid moves sometimes toward the
> edge of the box,sometimes towards the corners and so on...
>  Now how can i centre only the amino-acid to the centre of the box and rest
> (ie.,solvent mixture) to move as it is..ie., if i view the trajectory in
> vmd i want to fix only the amino-acid to be in centre,whereas the solvent
> mixtures to move around during the trajectory...
> How can i do this,...??
>
> Thank you...
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
>  referral=cy16f01.di...@nitk.edu.in=22>
> --
> 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.
>



-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

-- 
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.

[gmx-users] Regarding centering the molecule/protein during Simulation

2017-05-28 Thread Dilip H N 
Hello,
I have ran a md simulation of a amino-acid with solvent mixture. Now i view
the trajectory in vmd and see tht the amino-acid moves sometimes toward the
edge of the box,sometimes towards the corners and so on...
 Now how can i centre only the amino-acid to the centre of the box and rest
(ie.,solvent mixture) to move as it is..ie., if i view the trajectory in
vmd i want to fix only the amino-acid to be in centre,whereas the solvent
mixtures to move around during the trajectory...
How can i do this,...??

Thank you...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

-- 
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.