Re: [gmx-users] Gmx_solvate

2018-04-21 Thread Justin Lemkul 



On 4/21/18 3:16 AM, rose rahmani wrote:

But the box size is 4 4 12 and i should make an index for about 2000 SOL.
Is there any better solution?


What I suggested before is the only thing you can do. Learn to use gmx 
select, select the water molecules that satisfy your geometric (or 
whatever other) criteria and save them as an index group, then use 
trjconv to extract those coordinates.


-Justin



On Mon, 16 Apr 2018, 17:34 Justin Lemkul,  wrote:



On 4/16/18 8:51 AM, rose rahmani wrote:

Thank you so much.
You mean first use gmx solvate, then delete the Sol molecules which i

dont

need them?

Yes.


So trjorder can fix the rest, yes?

No, but trjconv can save what you want based on an index group from gmx
select.

-Justin


On Mon, 16 Apr 2018, 16:26 Justin Lemkul,  wrote:


On 4/16/18 5:58 AM, rose rahmani wrote:

Hi,

I have input structure from my last simulation. The box is 12nm long

in Z

axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8

to

12 is empty) .  I want to add solvent between z=3-8. How can i do that?
The problem is that i cant adjust wall and sheet( z coordination) to

start

from z=0 of box.
I mean when i extract wall and sheet from my last simulation and open

it

in

a viewer they wont start from 0, which is not odd. So i cant use the

box

size 0 to 5(8-3) in z dimension, use gmx_solvate and then make the box
larger.
What is your idea? Is there any tool to add solvate in specific

dimensions?

No.


Would you please help me?

Write a script to remove solvent molecules based on coordinates, or use
gmx select write an index group to do the same.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] Gmx_solvate

2018-04-21 Thread rose rahmani 
But the box size is 4 4 12 and i should make an index for about 2000 SOL.
Is there any better solution?


On Mon, 16 Apr 2018, 17:34 Justin Lemkul,  wrote:

>
>
> On 4/16/18 8:51 AM, rose rahmani wrote:
> > Thank you so much.
> > You mean first use gmx solvate, then delete the Sol molecules which i
> dont
> > need them?
>
> Yes.
>
> > So trjorder can fix the rest, yes?
>
> No, but trjconv can save what you want based on an index group from gmx
> select.
>
> -Justin
>
> > On Mon, 16 Apr 2018, 16:26 Justin Lemkul,  wrote:
> >
> >>
> >> On 4/16/18 5:58 AM, rose rahmani wrote:
> >>> Hi,
> >>>
> >>> I have input structure from my last simulation. The box is 12nm long
> in Z
> >>> axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8
> >> to
> >>> 12 is empty) .  I want to add solvent between z=3-8. How can i do that?
> >>> The problem is that i cant adjust wall and sheet( z coordination) to
> >> start
> >>> from z=0 of box.
> >>> I mean when i extract wall and sheet from my last simulation and open
> it
> >> in
> >>> a viewer they wont start from 0, which is not odd. So i cant use the
> box
> >>> size 0 to 5(8-3) in z dimension, use gmx_solvate and then make the box
> >>> larger.
> >>> What is your idea? Is there any tool to add solvate in specific
> >> dimensions?
> >>
> >> No.
> >>
> >>> Would you please help me?
> >> Write a script to remove solvent molecules based on coordinates, or use
> >> gmx select write an index group to do the same.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Virginia Tech Department of Biochemistry
> >>
> >> 303 Engel Hall
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==
> >>
> >> --
> >> 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.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Gmx_solvate

2018-04-16 Thread Justin Lemkul 



On 4/16/18 8:51 AM, rose rahmani wrote:

Thank you so much.
You mean first use gmx solvate, then delete the Sol molecules which i dont
need them?


Yes.


So trjorder can fix the rest, yes?


No, but trjconv can save what you want based on an index group from gmx 
select.


-Justin


On Mon, 16 Apr 2018, 16:26 Justin Lemkul,  wrote:



On 4/16/18 5:58 AM, rose rahmani wrote:

Hi,

I have input structure from my last simulation. The box is 12nm long in Z
axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8

to

12 is empty) .  I want to add solvent between z=3-8. How can i do that?
The problem is that i cant adjust wall and sheet( z coordination) to

start

from z=0 of box.
I mean when i extract wall and sheet from my last simulation and open it

in

a viewer they wont start from 0, which is not odd. So i cant use the box
size 0 to 5(8-3) in z dimension, use gmx_solvate and then make the box
larger.
What is your idea? Is there any tool to add solvate in specific

dimensions?

No.


Would you please help me?

Write a script to remove solvent molecules based on coordinates, or use
gmx select write an index group to do the same.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Gmx_solvate

2018-04-16 Thread rose rahmani 
Thank you so much.
You mean first use gmx solvate, then delete the Sol molecules which i dont
need them?
So trjorder can fix the rest, yes?

On Mon, 16 Apr 2018, 16:26 Justin Lemkul,  wrote:

>
>
> On 4/16/18 5:58 AM, rose rahmani wrote:
> > Hi,
> >
> > I have input structure from my last simulation. The box is 12nm long in Z
> > axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8
> to
> > 12 is empty) .  I want to add solvent between z=3-8. How can i do that?
> > The problem is that i cant adjust wall and sheet( z coordination) to
> start
> > from z=0 of box.
> > I mean when i extract wall and sheet from my last simulation and open it
> in
> > a viewer they wont start from 0, which is not odd. So i cant use the box
> > size 0 to 5(8-3) in z dimension, use gmx_solvate and then make the box
> > larger.
> > What is your idea? Is there any tool to add solvate in specific
> dimensions?
>
> No.
>
> > Would you please help me?
>
> Write a script to remove solvent molecules based on coordinates, or use
> gmx select write an index group to do the same.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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.
>
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Re: [gmx-users] Gmx_solvate

2018-04-16 Thread Justin Lemkul 



On 4/16/18 5:58 AM, rose rahmani wrote:

Hi,

I have input structure from my last simulation. The box is 12nm long in Z
axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8 to
12 is empty) .  I want to add solvent between z=3-8. How can i do that?
The problem is that i cant adjust wall and sheet( z coordination) to start
from z=0 of box.
I mean when i extract wall and sheet from my last simulation and open it in
a viewer they wont start from 0, which is not odd. So i cant use the box
size 0 to 5(8-3) in z dimension, use gmx_solvate and then make the box
larger.
What is your idea? Is there any tool to add solvate in specific dimensions?


No.


Would you please help me?


Write a script to remove solvent molecules based on coordinates, or use 
gmx select write an index group to do the same.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
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[gmx-users] Gmx_solvate

2018-04-16 Thread rose rahmani 
Hi,

I have input structure from my last simulation. The box is 12nm long in Z
axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8 to
12 is empty) .  I want to add solvent between z=3-8. How can i do that?
The problem is that i cant adjust wall and sheet( z coordination) to start
from z=0 of box.
I mean when i extract wall and sheet from my last simulation and open it in
a viewer they wont start from 0, which is not odd. So i cant use the box
size 0 to 5(8-3) in z dimension, use gmx_solvate and then make the box
larger.
What is your idea? Is there any tool to add solvate in specific dimensions?
Would you please help me?

Best regards
-- 
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