# Using gmx solvate with any generic solvent/how to solvate simulation efficiently

**URL:** <https://gromacs.bioexcel.eu/t/using-gmx-solvate-with-any-generic-solvent-how-to-solvate-simulation-efficiently/2813>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [September 14, 2021, 8:02pm UTC](https://gromacs.bioexcel.eu/t/using-gmx-solvate-with-any-generic-solvent-how-to-solvate-simulation-efficiently/2813 "2021-09-14T20:02:36Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![megamence](https://avatars.discourse-cdn.com/v4/letter/m/5e9695/32.png) [@megamence](https://gromacs.bioexcel.eu/u/megamence)\
**Post date:** [September 14, 2021, 8:02pm UTC](https://gromacs.bioexcel.eu/t/using-gmx-solvate-with-any-generic-solvent-how-to-solvate-simulation-efficiently/2813/1 "2021-09-14T20:02:36Z")

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GROMACS version: 2019.6  
GROMACS modification: No

I am trying to create a simulation box with a protein solvated in a particular solvent. I know gmx sovlate with spc216 exists, and is pretty fast. However, if I want to use another solvent like methanol, or ethanol, or hexane, etc. I don’t know if there is an easy, fast way to do this in gromacs.

At the moment, I have a methanol.pdb, methanol.itp and methanol.gro file, but when I do  
gmx solvate -cp protein.gro -cs methanol.gro -o protein-solvated.gro -p topol.top

I get zero methanol molecules added to my box. If I replace methanol.gro with spc216.gro, it fills it up instantly with 10000 water molecules (box is 7_7_7 nm^3), nearly instantly.

At the moment, I am using insert-molecules -nmol 5000 -try 10000 to solvate my protein with ethanol. However, this is taking a long period of time. Is there an efficient way to perform this task, given any generic solvent?

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [September 15, 2021, 1:42am UTC](https://gromacs.bioexcel.eu/t/using-gmx-solvate-with-any-generic-solvent-how-to-solvate-simulation-efficiently/2813/2 "2021-09-15T01:42:16Z")

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> [@megamence](#):
>
> I get zero methanol molecules added to my box

Do you mean the coordinate file has no methanol, or the topology? By default, `solvate` will print out that it added zero molecules but that’s because it’s programmed to only print out statistics about SOL molecules (water) and only update the topology automatically in that case. It should be adding them to the coordinate file but not the topology (i.e. there is no point in passing the `-p` option here because it will do nothing).

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<div class="post-metadata">

**Author:** ![megamence](https://avatars.discourse-cdn.com/v4/letter/m/5e9695/32.png) [@megamence](https://gromacs.bioexcel.eu/u/megamence)\
**Post date:** [September 15, 2021, 3:01am UTC](https://gromacs.bioexcel.eu/t/using-gmx-solvate-with-any-generic-solvent-how-to-solvate-simulation-efficiently/2813/3 "2021-09-15T03:01:15Z")

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Both: solvate is printing out that nothing was added, and I open the .gro file, protein-solvated .gro and I see no methanol in there.

I have a 7x7x7 box with one polymer chain inside it, and then I am trying to introduce the following methanol.gro:

```auto
METHANOL
    6   
    0MS C01 1 46.733 67.333 2.700
    0MS O02 2 46.733 49.033 48.200
    0MS H03 3 46.633 21.333 22.600
    0MS H04 4 46.633 20.933 78.900
    0MS H05 5 46.733 59.933 93.800
    0MS H06 6 46.733 61.633 34.000
  93.40005 93.40005 93.40005

```

the pdb file I editconf’d to get this file was:

```auto
COMPND METHANOL
AUTHOR GENERATED BY OPEN BABEL 2.3.90
ATOM 1 C01 MSOL 1 -0.743 0.003 0.025 1.00 0.00 C99 
ATOM 2 O02 MSOL 1 0.560 0.458 -0.292 1.00 0.00 O96 
ATOM 3 H03 MSOL 1 -1.283 -0.202 -0.902 1.00 0.00 H98 
ATOM 4 H04 MSOL 1 -1.279 0.765 0.598 1.00 0.00 H98 
ATOM 5 H05 MSOL 1 -0.669 -0.914 0.615 1.00 0.00 H98 
ATOM 6 H06 MSOL 1 0.686 1.316 0.147 1.00 0.00 H97 
CONECT 1 3 2 4 5    
CONECT 2 1 6    
CONECT 3 1    
CONECT 4 1    
CONECT 5 1    
CONECT 6 2    

```

Could this lead to a problem?

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [September 15, 2021, 4:46pm UTC](https://gromacs.bioexcel.eu/t/using-gmx-solvate-with-any-generic-solvent-how-to-solvate-simulation-efficiently/2813/4 "2021-09-15T16:46:13Z")

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`solvate` assumes you are passing a box of pre-equilibrated solvent via `-cs`, not a single molecule.

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<div class="post-metadata">

**Author:** ![megamence](https://avatars.discourse-cdn.com/v4/letter/m/5e9695/32.png) [@megamence](https://gromacs.bioexcel.eu/u/megamence)\
**Post date:** [September 18, 2021, 11:38pm UTC](https://gromacs.bioexcel.eu/t/using-gmx-solvate-with-any-generic-solvent-how-to-solvate-simulation-efficiently/2813/5 "2021-09-18T23:38:39Z")

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I understand. Thank you for your advice!