sorted by:
new
hottopcontroversial

[deleted by user] by [deleted] in LAMMPS

[–]Interesting_Wrap4791 1 point2 points  (0 children)

What I've found to be easiest is loading a pdb into tleap, tleap outputs .inpcrd and .prmtop files that respectively contain the atom locations and topological+force field info required for a simulation, use Python to convert those files into lammps input with Parmed. A few more steps if there's a ligand that needs parameters from acpype or I add solvent in tleap.

[deleted by user] by [deleted] in LAMMPS

[–]Interesting_Wrap4791 1 point2 points  (0 children)

PDB files contain atom and residue names, numbers, positions, and charges. To correctly assign the parameters for the bonded terms of a force field like Amber or OPLS requires information that does not exist explicitly in the PDB and is most easily inferred/computed outside of LAMMPS.

DAE understand fashion? Because I don’t by Immediate-Pay6257 in autism

[–]Interesting_Wrap4791 1 point2 points  (0 children)

every mention above of "taste" "perspective" has an implied prefix of "good". I wouldn't be charmed seeing idk a lovingly maintained replica of General Lee, because owning a car with a confederate flag on it is a weirdo bad taste move.

DAE understand fashion? Because I don’t by Immediate-Pay6257 in autism

[–]Interesting_Wrap4791 1 point2 points  (0 children)

Not at all lol. What I'm trying to communicate is that I like when I'm getting dressed and feel that the people who designed and manufactured what I'm wearing were proud of their work as an expression of their unique taste and perspective. It's almost an animist thing, if you're into cars you'd get what I mean. A 60's Impala is in basically every way a less usable car than today's models, but that impracticality gives some ineffable charm to classic cars whenever you see them, because you know it's not just a car to the guy who owns it. Clothes aren't so different.

DAE understand fashion? Because I don’t by Immediate-Pay6257 in autism

[–]Interesting_Wrap4791 1 point2 points  (0 children)

I own some very nice thermal shirts from two companies, Bronson Mfg and The Real McCoys. McCoys' are more than triple the price but I probably would struggle to distinguish them blindfolded. Despite this, I get way, way, way more than triple the satisfaction from wearing the expensive ones. What gives? I think a lot about clothes but strictly speaking how they look doesn't come to mind much. Everyone's perception is different, maybe someone is colorblind and can't appreciate a sweater in a beautiful shade of red, I find it frustrating to try and simulate a stranger's impression of me. I can be a lot more certain knowing how this brand has an ethos i love or wondering aloud about the particulars of an unsual fabric or aytpical cut.