# [gmx-users] Gmx_solvate

Justin Lemkul jalemkul at vt.edu
Sat Apr 21 14:40:03 CEST 2018

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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, <jalemkul at vt.edu> 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, <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.
>>>>
>>>> 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
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> Gromacs Users mailing list
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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
>>
>> ==================================================
>>
>> --
>> 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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>>

--
==================================================

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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