[gmx-users] A problem regarding simulation of SiO2

[Lianqing Zheng]

Dear Gromacs team:

I encountered two problems running Gromacs to simulate Silica(SiO2). First
one is use pdb2gmx to produce .top or .gro file. The error is:
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Fatal error: Residue 'UNK' not found in residue topology database.
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(I used "UNK" as residue name in the .pdb file.)

After I changed "UNK" to "SOL", the error became:
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Fatal error: Atom SI in residue HOH 1 not found in database
             while sorting atoms
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So I created my own .top and .gro files but got the second problem when
using grompp command to get .tpr file:
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processing topology...
Warning 1 [file "fs.top", line 16]:
  Too few parameters on line (source file toppush.c, line 170)
Warning 2 [file "fs.top", line 17]:
  Too few parameters on line (source file toppush.c, line 170)
Cleaning up temporary file /var/tmp/aaaXTayPY
Fatal error: Atomtype 'O' not found!
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My .top file is as follows:
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[ defaults ]
2 1
[ atomtypes ]
;name        mass      charge   ptype            c6           c12
    O    15.99940       -1.20        A   	0.22617E-02   0.74158E-06
   SI    28.08000        2.40        A   	0.14738E-01   0.22191E-04
[ nonbond_params ]
  ; i    j func           a             b	c6
    O    O    2 1.339973E+5	     27.6	1.688507E-2
    O	SI    2 1.737112E+6	  48.7318	1.288457E-2
   SI	SI    2		0.0	      0.0	0.0
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The potential I use is just Buckingham and Coulomb. There is no bonded
interaction.

Could you help me with these problems?

Thanks a lot!

Lianqing Zheng
Graduate Student
University of Rochester
Rochester, NY, USA