[gmx-users] Gmx_solvate

[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, <jalemkul at vt.edu> 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
>>
>> jalemkul at 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

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

==================================================