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Nike Dattani
Nike Dattani
8:27 AM
@mykd :
4
A: Generalized Born implicit solvent models and pairwise descreening

Don Truhlar This would seem to result in a very large relative error in calculated GB radius. How is this approximation okay? The systematic error is corrected in an average way by the scale parameters on page 125 of the Hawkins et al. paper. Are there any systematic studies of the degree of error this in...

 
 
6 hours later…
LAMMPS Forum
LAMMPS Forum
2:13 PM
LAMMPS - Materials Science Community Discourse: Building structures for lammps input
posted on February 04, 2023 by Runak_R

Dear Lammps Users, How can I build a molecule structure data file for LAMMPS simulations? For example a complex structure of a chemical drug. which software is the best? and If I want to functionalize a structure such as graphene with amine group, Is it OK to construct separate structures and let them to be adsorbed during simulation spontaneously? If not how we can functionlize st…

 
 
2 hours later…
LAMMPS Forum
LAMMPS Forum
3:55 PM
LAMMPS - Materials Science Community Discourse: Pressure showing as -nan
posted on February 04, 2023 by mps

dear all， I’m running a reaxff program but an error occurs. ERROR on proc 1: Non-numeric atom coords - simulation unstable, I noticed the press showing as -nan, this may be the reason but I do not know how to fix it. Attached please find my in.file and forcefield file and log file. the OS I’m using is Ubuntu 20.04.5 LTS, the LAMMPS version is lammps-10Mar21. Besides, if decreasi…

LAMMPS - Materials Science Community Discourse: How to understand "group-ID" in "fix ID group-ID gcmc N X M type seed T mu displace"
posted on February 04, 2023 by lltll123

Dear all hi, the lammps users .I want to ask you a question about gcmc command. fix ID group-ID gcmc N X M type seed T mu displace fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01 For the fix, where is the area to simulate exchanging and moving? If it is my box by default, what is “group-ID” in “fix gcmc”? If it is understood as the part to be fixed, but I have only done “gro…

 
 
3 hours later…
mykd
mykd
6:25 PM
@NikeDattani Hi @NikeDattani, I didn't exactly understand your message. Do you me to comment on the question? It's a bit outside my area.
 
Nike Dattani
Nike Dattani
6:35 PM
@mykd did you see the user that answered it? :) :)
 
 
1 hour later…
mykd
mykd
7:38 PM
@NikeDattani Are you sure it's him? He is not as online as others, even compared to Nesse, Grimme, or Hutter.
 
Nike Dattani
Nike Dattani
7:58 PM
@mykd it's him! He emailed me.
 
mykd
mykd
Oh ok.
 
Nike Dattani
Nike Dattani
@mykd the contents of this email are the same as the contents of the SE post. Tyberius just needed to edit the formatting a bit.
 
mykd
mykd
Yeah, he is much more responsive to emails in that sense.
 
Nike Dattani
Nike Dattani
I just requested for him to post it on MMSE. I don't know the user or anything about the question, but I wanted to help them get an answer.
 
mykd
mykd
Oh so the user account isn't Don's. It is Tyberius posting for Don.
 
 
2 hours later…
Nike Dattani
Nike Dattani
9:51 PM
@mykd No it's Don's account! I replied to Don's email, asking him to answer the question on MMSE. The next morning, the answer was there with an account named "Don Truhlar". But he didn't format it properly, so Tyberius edited the answer to fix the formatting.
Tyberius never saw this email, the only person that could have posted this was Don. The post was exactly the same as the email.
 

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