[gmx-users] Preparing a silicon bulk

Justin Lemkul jalemkul at vt.edu
Fri Dec 19 23:11:26 CET 2014

On 12/19/14 12:43 PM, Kevin C Chan wrote:
> 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?

Replies work like any other email.  Click reply, change the subject, chop out 
the text that doesn't pertain to your issue, and send.  If digests are acting 
weird, switch to individual messages.  The list can be somewhat high-traffic, 
but certainly the last few weeks haven't been all that busy.

> 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?

Si should form 4 bonds; that's what satisfies its valence.  What g_x2top is 
telling you is: "I found 4 atoms within the bond distance, but you tell me in 
the .n2t file that there should only be 3."

The Si parameters in the force field were probably for silica, so no Si-Si bonds.

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

In theory, you have a regular ordering of atoms on a lattice, so g_x2top is the 
perfect tool, but the desire to assign different charges makes that difficult. 
I would suggest building the topology with g_x2top and modifying as needed; that 
will require some scripting (or could be done by hand for a reasonably small 
system), but realize that changes in charges can affect the validity of bonded 
parameters, since everything in a force field is interconnected.  So even if you 
find suitable bonded parameters for the interactions you need, if you change 
aspects of the nonbonded parameters, the bondeds can be compromised as a result...



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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