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I have a .pdb file containing water molecules.

TITLE     Generated by gmx solvate
REMARK    THIS IS A SIMULATION BOX
CRYST1   12.500   12.500   12.500  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM      1  OW  SOL     3       5.300  10.220   4.860  1.00  0.00
ATOM      2  HW1 SOL     3       6.200   9.970   4.700  1.00  0.00
ATOM      3  HW2 SOL     3       5.260  11.150   4.630  1.00  0.00
ATOM      5  OW  SOL     4       8.140   4.780   4.990  1.00  0.00
ATOM      6  HW1 SOL     4       7.890   5.660   5.270  1.00  0.00
ATOM      7  HW2 SOL     4       8.110   4.810   4.030  1.00  0.00
ATOM      9  OW  SOL     5       2.560   5.060   4.270  1.00  0.00
ATOM     10  HW1 SOL     5       2.880   5.940   4.090  1.00  0.00
ATOM     11  HW2 SOL     5       2.440   5.040   5.220  1.00  0.00
ATOM     13  OW  SOL     6       3.340   9.190  13.280  1.00  0.00
ATOM     14  HW1 SOL     6       3.970   8.660  12.790  1.00  0.00
ATOM     15  HW2 SOL     6       3.150   9.930  12.710  1.00  0.00
ATOM     17  OW  SOL     7       6.550   2.610   5.140  1.00  0.00
ATOM     18  HW1 SOL     7       7.130   3.370   5.160  1.00  0.00
ATOM     19  HW2 SOL     7       5.900   2.820   4.470  1.00  0.00

I want to generate the charges on these atoms using gromacs. What commands will i run with which force-field to do this ?

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  • 2
    $\begingroup$ water FF parameters are stored in itp files. Gromacs looks them up when you tell gromacs the water model, or, you just supply the itp file yourself since they are readily available for all of the common water models $\endgroup$
    – Wesley
    Feb 26, 2022 at 14:54
  • $\begingroup$ There is something funny about your numbering. Where is atom 4, 8, 12, 16 $\endgroup$
    – Wesley
    Feb 27, 2022 at 23:09
  • 1
    $\begingroup$ I had generated a gro file using gmx solvate for tip4p. Had to remove the 4th line to create an xyz file from it $\endgroup$
    – fireball.1
    Mar 5, 2022 at 11:47

1 Answer 1

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GROMACS keeps internal topology files for common water models. You are clearly using a 3-point water model such as spc, spc/e, tip3p, OPC3 etc. You can also supply your own topology file. Here is a full topology file. Often, molecule parameters are stored in an itp file, since the topology has other stuff not specific to molecules, such as 1-4 interactions, simulation name, numbers of molecules etc. However, for an spc/e simulation, you could supply this topology

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1             2               yes             0.5       0.8333

[ atomtypes ]
;         name   mass      charge     ptype    sigma(nm)     epsilon(kJ/mol)  
; SPC/E atoms  
O1        O1    15.99940   -0.8476      A       0.3166       0.6500000 
H         H     1.008000   0.4238       A       0.0000       0.0000000 


[ moleculetype ]
SOL     2

[ atoms ]
 1   O1   1  SD    OW    1    -0.8476   15.99940
 2   H    1  SD    HW1   1     0.4238   1.00800
 3   H    1  SD    HW2   1     0.4238   1.00800

#ifndef FLEXIBLE

[ settles ]
;OW  funct   doh   dhh
1      1     0.1    0.16330

[ exclusions ]
1    2    3
2    1    3
3    1    2

#else

[ bonds ]
;   i    j    funct    length    force.c
1    2         1        0.1          345000
1    3         1        0.1          345000

[ angles ]

  i   j   k   funct   angle   force.c
 2    1    3     1    109.47   383

#endif
 
[ system ]
spce

[ molecules ]
SOL 5

Note that all oxygens will have charge of -0.8476 and all hydrogens will have charge of 0.4238. Different water models will have different charges, but all oxygens and hydrogens in waters will have uniform charges.

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  • $\begingroup$ are you aware if i can generate an .itp file using pdb2gmx for my pdb file $\endgroup$
    – fireball.1
    Mar 5, 2022 at 9:43
  • $\begingroup$ I am pretty sure you can, but I have never done it that way. Gromacs is largely made for simulating proteins, which I don't do, so I have never used that built in machinery, but, I am almost positive it exists. Check out Justin Lemkul's tutorials mdtutorials.com/gmx $\endgroup$
    – Wesley
    Mar 5, 2022 at 23:22
  • $\begingroup$ Is there some other way you are aware of ? My eventual goal is to have the charges of each atom and then visualize it in pmepot (VMD plugin) $\endgroup$
    – fireball.1
    Mar 6, 2022 at 10:53
  • $\begingroup$ Is your system only water, or does it have a solute(s) in it? $\endgroup$
    – Wesley
    Mar 6, 2022 at 12:03
  • $\begingroup$ It's just water $\endgroup$
    – fireball.1
    Mar 6, 2022 at 18:40

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