Dears LAMMPS support and community,
I am a new user of LAMMPS, moltemplate and VMD.
The solvent I am using here is Ethyl acetate. its chemical structure is attached (fig 1).
So I have generated a topology file using moltemplate using the OPLSaa force field to assign the type of the atoms and charge. Then I used topotool to visualize the molecule and check if I did that correctly. Fig2 shows how it appeared on VMD (attached document). The double bond didn’t show although the atom types assigned were correct. which is my first question is this normal, should I be concerned? The colour is assigned to the atom type, apparently, the PSF file from topotool doesn’t have information about the atom name (H, C, O … etc).
After running the files on the LAMMPS and loading the trajectory file, the hydrogen atoms attached to each other with bonds, please see fig 3. this occurred only with the hydrogen that attached to the same atom for example the hydrogen in the methyl group attached with each other. So I just want to know if this is normal and what should I check if it is a problem?
I apologize if this issue is discussed earlier but I have searched a lot and the keywords for these issues cannot help to narrow down the search results enough to find the answer. Thanks for your help.
Best regards,
Moulham
Ethyle-acetate .pdf (83.1 KB)
for the most part, these are questions about using VMD, not LAMMPS, so in the future you may be better off asking similar questions in the future on the VMD mailing list, not here.
a) double bonds. there is no information about bond order in any of the file formats you are using, so VMD cannot display what is not there. it doesn’t do it for most representations, anyway.
b) colors and elements. unless you give VMD a helping hand, it has no idea about what element which atom type represents. it just sees a number and it will (in a desperate attempt to make sense of those) assume that each number represents the index of the element in the periodic table (which is grossly wrong).
c) recovering element information. if you have a data file, you have atom masses and if those are “normal” you can use the topotools plugin to “guess” element names from masses. you can then also “guess” the name field from the element and the atom radius from the element. colors are likely to be off due to some low-level bug in VMD (or how topotools interacts with VMD) that nobody has figured out yet. but you can save a .psf file (for visualization purposes) and if you load that back and add coordinates with a lammps trajectory file, you will get the expected coloring.
d) unexpected bonds. this happens when you are loading the lammps trajectories file(s) without a suitable .psf file first. the trajectory file has no topology information and also no element information (unless you use dump_modify and dump the element name, which is wasteful, better to use a .psf file). at this point VMD does not know you have hydrogen atoms and will assign bonds without consideration of the number of valences.
HTH,
axel.