[gmx-users] Preparing a silicon bulk

[Kevin C Chan]

I am kind of confused, how could I actually reply and include my reply into a thread in the mailing list? As I am receiving digest email, I should not just press the reply bottom, or should I?

Back to the question, thank you for providing the hint on unit of Gromacs, g_x2top could identify the bonds now. However g_x2top is still not working as:

Opening force field file /home/kevin/opt/gmx_fftw3_double/share/gromacs/top/gromos54a7.ff/atomname2type.n2t
There are 1 name to type translations in file gromos54a7.ff
Generating bonds from distances...
atom 8
Can not find forcefield for atom SI1-1 with 4 bonds
Can not find forcefield for atom SI2-2 with 4 bonds
Can not find forcefield for atom SI3-3 with 4 bonds
Can not find forcefield for atom SI4-4 with 4 bonds
Can not find forcefield for atom SI5-5 with 4 bonds
Can not find forcefield for atom SI6-6 with 4 bonds
Can not find forcefield for atom SI7-7 with 4 bonds
Can not find forcefield for atom SI8-8 with 4 bonds

And my atonname2type.n2t contains:
SI   SI         1     28.08   3    SI 0.2352     SI 0.2352      SI 0.2352

We could see that it identifies 4 bonds for each atom (but why not 3?), however no ff could be found. I look into gromos54a7 (I thought it contains Si forcefields) and I found no Si-Si bonded parameters in ffbonded.itp but a comprehensive set of non-bonded parameters of Si in ffnonbonded.itp. I am curious why it is like this. Did people only do single Si simulations?

Ultimately is it better (or easier) to manually construct the topology file?

Regards,



On 12/18/14 11:46 PM, Kevin C Chan wrote:
> Due to some reasons I could not receive digests from the list so I could
> only copy and paste from the archives and reply to you. I really hope this
> reply could go to the same thread of my question so it would not screw the
> list archive.
> 

Nope, this is the start of a new thread now.  Make sure you sort out whatever delivery issues you're having using the admin page.

> Back to the question, first thank you so much for your reply Justin. I
> understand that pdb2gmx might not be useful, I just tried it. g_x2top seems
> better but I could not get it work even following the file format: it says
> it could find 1 name to type translations but it can not find forcefield
> for atoms like
> 
> Opening force field file
> /home/kevin/opt/gmx_fftw3_double/share/gromacs/top/gromos54a7.ff/atomname2type.n2t
> There are 2 name to type translations in file gromos54a7.ff
> Generating bonds from distances...
> atom 8
> Can not find forcefield for atom SI1-1 with 0 bonds
> Can not find forcefield for atom SI2-2 with 0 bonds
> Can not find forcefield for atom SI3-3 with 0 bonds
> Can not find forcefield for atom SI4-4 with 0 bonds
> Can not find forcefield for atom SI5-5 with 0 bonds
> Can not find forcefield for atom SI6-6 with 0 bonds
> Can not find forcefield for atom SI7-7 with 0 bonds
> Can not find forcefield for atom SI8-8 with 0 bonds
> 
> 
> I gave the n2t like
> 
> SI   SI         1     28.08   3    SI 2.352     SI 2.352      SI 2.352
>  ;2.352 is measured from my input coordinates
> 

Gromacs uses nm for everything, not Angstrom.  Given that bonds are detected based on a 10% distance tolerance, this is the reason for the above messages.

> 
> and just trying with 8 SI atoms and in the future I definite would like to
> have more.
> 
> 
> While waiting for your comments on this g_x2top problem, I would also like
> to have suggestions on manually writing the top file. As I don't think we
> need those tedious dihedrals for a silicon bulk, I though the topology
> should look rather simple:
> 
> #include "gromos54a7.ff"
> ; I have looked into gromos54a7 and found parameters for SI so this include
> is enough am I right?
> [ moleculetype ]
> ; name SomeName
> SI 8
> [ atoms ]
> 1  SI  1  SI  SI1  1  charge1
> 2  SI  1  SI  SI1  1  charge2
> ...
> 8  SI  1  SI  SI1  1  charge8
> ; Maybe bonds and angles are also needed? I am not sure

You need to determine a suitable force field based on something that is published and validated to work.  I don't know what the source of Si parameters is for Gromos96, but people use different force fields in published work.  If you're wondering if bonds and angles are necessary (certainly the former, likely the latter, and maybe/maybe not on dihedrals, depending on the parametrization) then you need to back up and do some evaluation of parameters that are already available.  The output is only as good as the input, and Gromacs tools won't work (too much) magic to save you from mistakes.

-Justin

> #include "spc.itp"
> [ system ]
> SomeName
> 
> [ molecules ]
> SI 8
> SOL 100
> 
> 
> 
> Is this the case?
> 
> 
> Thanks in advance,
> 
> Kevin


Kevin
ukevi at gmx.hk