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

User discussions
1

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 777 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?

2

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).

3

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:

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:

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?

4

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

5

I understand. Thank you for your advice!