[gmx-users] Atom names mismatch

[George Abadir]

Thank you very much for your help, I appreciate it very much :)
I redid one of the simulations. The initial temperature and the 
temperature at the different early time steps is also slightly 
different. The final structure of the moleculeis exactly like the input 
(i.e., the aromatic ring is preserved, no atoms have exchanged their 
places). By checking the energies, I can see that the total energy, 
Coulombic, potential and kinetic energies are almost identical 
throughout the whole simulation, not only for few steps. The bond energy 
and dihedral energies, howver, differ a bit. I use the "optimize_fft" 
option and I had read before that this may lead to different results for 
the same time steps. When you said "the energy numbers", did you mean 
all the energies, or the total energy is a sufficient indicator for the 
correctness of the result.
Thanks alot and appreciate your help,
Regards,
George

Mark Abraham wrote:

> George Abadir wrote:
>
>> Thanks for your reply. I built the molecule using PYMOL, then used 
>> pdb2gmx to generate the topology. It seems that pdb2gmx reorders the 
>> atoms. Then in the simulation I used the initial PDB file generated 
>> by PYMOL. 
>
>
> Right. Don't do this. For input to grompp and/or other GROMACS tools, 
> use the structure that pdb2gmx writes out, since that is now 
> consistent with the re-ordering in the topology. This will immediately 
> solve the issue for the future. In future, generate your topologies 
> interactively, and check for warnings, etc before running simulations.
>
> You can partly validate, or possibly totally invalidate the old 
> simulations by doing a quick repeat calculation with a correct match 
> of topology and starting structure. If valid, the logfile energy 
> numbers should remain identical for several picoseconds. If not valid, 
> they'll diverge in that time.
>
>> Does this make things any more reasonable. Because actually, this 
>> happened in five different simulations till now!!!! So, I don't think 
>> it is a mere coincidence. The molecule at the end is intact and all 
>> the atoms are in their respective positions (i.e., the carbon was not 
>> actually exchanged with hydrogen as it should be from the warning). 
>> It would very helpful if someone could see how these simulations 
>> continued without deforming the molecule.
>
>
> Mark
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