[gmx-users] vsite problem in gromacs 4.0

[Berk Hess]

Hi,

You can not do much.
The reason for this error message is also valid for older versions.
It can not be guaranteed that the virtual sites in one charge group will
have the same periodic shift. But before 4.0 there was no check for this.

I would simply not use vsite aromatics. I am in favor of completely
removing this option from pdb2gmx, since you do not gain so much
compared with dt=4 or 5 fs with -vsite h (and optionally heavy hydrogens).

If you really want to use the vsite aromatics, you can put all atoms
in the aromatic groups in separate charge groups, but that will make
the simulation slightly slower.

Berk


> Date: Tue, 4 Nov 2008 02:45:13 -0800
> From: zazeri at yahoo.com.br
> To: gmx-users at gromacs.org
> Subject: [gmx-users] vsite problem in gromacs 4.0
> 
> Hi gmx-users!
>  
> I've created the topology of a peptide using pdb2gmx(4.0-rc4) converting aromatic rings into virtual sites. I've used the grompp(4.0_rc4) to compile the input for the mdrun and it was ok, no error message, but
> when running mdrun(4.0-rc4):
> 
> Program mdrun4, VERSION 4.0_rc4
> Source code file: vsite.c, line: 1504
> 
> Fatal error:
> Virtual site atom 29 is part of a charge group of only virtual sites, but its first constructing atom (26) is part of a different charge group, this combination is not allowed.
> 
> I've repeated the process using grompp(3.3.1), mdrun(3.3.1) and the same topology (it was created by pdb2gmx(4.0-rc4)) and the simulation run well.
> 
> What could I do? I'd like enjoy the new implementations in PME from gromacs 4.0! Any suggestion would be appreciated, thanks. Fernando "Zazeri" Lopes.
> 
> 
> A little part from my topology (as GROMOS87):
> 23          N      3    TRP      N     12      -0.28  15.0147
> 24          H      3    TRP      H     12       0.28  0
> 25        CH1      3    TRP     CA     13          0  13.019
> 26         MW      3    TRP    MW1     14          0  52.0557
> 27         MW      3    TRP    MW2     14          0  64.087
> 28        CH2      3    TRP     CB     15          0  14.027
> 29         CB      3    TRP     CG     16      -0.14  0
> 30        CR5      3    TRP    CD1     16      -0.14  0
> 31        HCR      3    TRP    HD1     16       0.14  0
> 32         CB      3    TRP    CD2     16          0  0
> 33       NR5*      3    TRP    NE1     16      -0.05  0
> 34          H      3    TRP    HE1     16       0.19  0
> 35         CB      3    TRP    CE2     17          0  0
> 36        CR6      3    TRP    CE3     18      -0.14  0
> 37        HCR      3    TRP    HE3     18       0.14  0
> 38        CR6      3    TRP    CZ2     19      -0.14  0
> 39        HCR      3    TRP    HZ2     19       0.14  0
> 40        CR6      3    TRP    CZ3     20      -0.14  0
> 41        HCR      3    TRP    HZ3     20       0.14  0
> 42        CR6      3    TRP    CH2     21      -0.14  0
> 43        HCR      3    TRP    HH2     21       0.14  0
> 44          C      3    TRP      C     22       0.38  12.011
> 45          O      3    TRP      O     22      -0.38  15.9994
> 
> 
> 
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