Msi2lmp unable to find bond data (from MS to LAMMPS)

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1

Dear LAMMPS experts:

I built some crosslinked expoxy resin EPON 862 using Materials Studio and converted them using mis2lmp of lammps windows 64bit package (20170127). Based on cvff.frc in lammps, there are three warnings as follows:

Unable to find bond data for cp oc

Unable to find oop data for c2 na c2 c2

Unable to find oop data for c2 na c2 hn

I guess cp-oc bond is quite important in the molecule, so I checked the cvff.frc file trying to locate it from both “morse_bond” and “quadratic_bond”, but there is no data for cp-oc, or cp-o which seems to be an equivalence. More strange is that I then tried the cvff.frc bundled to MS and found all the warinings reported are exactly the same.

So does that mean the two cvff.frc files, in lammps and MS, respectivley, are the same ? Is there any other way to solve the problem about the bond data ? For example, editing the Msi2lmp program ?

The command based on lammps’s cvff.frc is attached:

“C:\Program Files\LAMMPS 64-bit 20170127\Msi2lmp\msi2lmp.exe” D:\Research\MDsimlation\Sketch4\Sketch6 -class 1 -f “C:\Program Files\LAMMPS 64-bit 20170127\frc_files\cvff.frc” -i

Many thanks for the great help !

Xu Hao

2

Dear LAMMPS experts:

I built some crosslinked expoxy resin EPON 862 using Materials Studio and
converted them using mis2lmp of lammps windows 64bit package (20170127).
Based on cvff.frc in lammps, there are three warnings as follows:

Unable to find bond data for cp oc

Unable to find oop data for c2 na c2 c2

Unable to find oop data for c2 na c2 hn

I guess cp-oc bond is quite important in the molecule, so I checked the
cvff.frc file trying to locate it from both "morse_bond" and
"quadratic_bond", but there is no data for cp-oc, or cp-o which seems to be
an equivalence. More strange is that I then tried the cvff.frc bundled to
MS and found all the warinings reported are exactly the same.

So does that mean the two cvff.frc files, in lammps and MS, respectivley,
are the same ? Is there any other way to solve the problem about the bond
data ? For example, editing the Msi2lmp program ?

​the important question here is: can you run the same system with MS using
cvff and get meaningful results?​

if yes, you would have to reverse engineer what MS is doing differently and
then try to implement this in msi2lmp.
your question is the last in a long line of rather similar inquiries. the
primary issue in all cases is, that msi2lmp was developed over 10 years ago
and has only been updated to remove bugs and stay compatible with LAMMPS by
people that don't have access to MS or necessarily care much about
expanding msi2lmp's functionality (since they don't need it themselves).

there are several known limitations in msi2lmp (for example no support for
alternate bonded interactions, i.e. morse instead of hardmonic, or no
support for auto-equivalences) that won't be removed unless somebody comes
along, that has both, sufficient interest in lifting those limitations and
sufficient expertise in C programming and reading/understanding C code, as
well as a sufficient understanding of the inner working of MS.

​the alternative would be to search the literature for suitable force field
parameters for your compound(s) and apply those manually.​

​axel.​

The command based on lammps's cvff.frc is attached:

3

Dear LAMMPS experts:

I built some crosslinked expoxy resin EPON 862 using Materials Studio and
converted them using mis2lmp of lammps windows 64bit package (20170127).
Based on cvff.frc in lammps, there are three warnings as follows:

Unable to find bond data for cp oc

Unable to find oop data for c2 na c2 c2

Unable to find oop data for c2 na c2 hn

I guess cp-oc bond is quite important in the molecule, so I checked the
cvff.frc file trying to locate it from both “morse_bond” and
“quadratic_bond”, but there is no data for cp-oc, or cp-o which seems to be
an equivalence.

If my understanding is correct, then check the “auto_equivalences” section of the “cvff.frc” file (lines 429, and 471 of that file. I am looking the version located in the “msi2lmp/frc_files/” subdirectory, not the official MSI on.)

Then take a look at lines 2195 and 2835 of that same file:

line 2195 (morse)
2.0 18 cp_ o_ 1.3700 96.0000 2.0000

line 2835 (quadratic)
2.0 18 cp_ o_ 1.3700 384.0000

(You probably want the first one.) In both cases, the bond-length is 1.3700

According to the Cerius2 (Discovery) documentation, “auto_equivalences” are used as a last resort when it can’t find (regular) equivalences which satisfy the pattern. Sometimes multiple different lines from the .frc file define bonds which satisfy the atom type requirements, and in that case, the version# and *-priority-number come into play. The Discovery/Cerius2 software can figure out which of these lines in the .frc file which satisfy the type pattern has the highest priority and use those parameters for that bond.

If my understanding is correct, the DiscoveryStudio/Cerius2 programs use BOND equivalences to lookup the equilibrium bond lengths used in the “bond-bond” and “bond-angle” terms (which appear in the angle interactions). (Similarly, ANGLE equivalences are used to lookup equilibrium angles in “angle-angle” “angle-angle-torsion” terms, which appear in improper and dihedral interactions.)

msi2lmp does not understand auto_equivalences sections in cvff.frc and pcff.frc. Additionally, msi2lmp also fails to find bonds for “compass_published.frc” as well, even though that file does not use “auto_equivalences”.

Mahdi, Shyam and I have been working on a version of the moltemplate molecule builder tool which can read .FRC files like “cvff.frc” and “pcff.frc”, “compass_unpublished.frc”, “dreiding.frc”, “uff.frc”, … However the current version of moltemplate sometimes fails to find bonds as well. This could be because the versions of these files which are bundled with msi2lmp are incomplete. (They are not the same as the official version.) I am hoping to find someone an official version of these FRC files that I can use just to test if moltemplate is reading these FRC correctly. (Please do not post it to the list.) When we can verify that moltemplate seems to be working with the official FRC files, we will post a message to the list, and share what information we can legally. (Until then we will not release it. I estimate this will take about 3 months because we are busy working on other projects at the moment.)

More strange is that I then tried the cvff.frc bundled to MS
and found all the warinings reported are exactly the same.

So does that mean the two cvff.frc files, in lammps and MS, respectivley,
are the same ?

As I recall, if you run “diff” on them, they are not quite the same, but I think they are of similar size.

Is there any other way to solve the problem about the bond
data ? For example, editing the Msi2lmp program ?

the important question here is: can you run the same system with MS using
cvff and get meaningful results?

That is what I would do.
If you have access to materials studio, I would use that program to run your simulations.

If you insist on running your simulations in LAMMPS, then try EMC, and be sure to check the DATA files that it creates carefully to see if they make sense.

I do not trust any of the free tools which support MSI force fields (except perhaps TOWHEE, but it does not support CVFF or PCFF).

if yes, you would have to reverse engineer what MS is doing differently and
then try to implement this in msi2lmp.

Use Materials Studio for now.

your question is the last in a long line of rather similar inquiries.

Yes, check out these posts:

[https://sourceforge.net/p/lammps/mailman/message/35698640/](https://sourceforge.net/p/lammps/mailman/message/35698640/)
[https://sourceforge.net/p/lammps/mailman/message/29578563/](https://sourceforge.net/p/lammps/mailman/message/29578563/)
[https://sourceforge.net/p/lammps/mailman/message/35700652](https://sourceforge.net/p/lammps/mailman/message/35700652)
[http://lammps.sandia.gov/threads/msg58456.html](http://lammps.sandia.gov/threads/msg58456.html)