Bro same... i was only getting the bonds and was so confused why it wasnt generating angles/dihedrals. saved my bacon after me searching for over 12 hours...
Hello, I am struggling with atom types of same element atoms which I need to denote differently in the Lammps data file from VMD. For example , in my pdb file there are 2 carbon atoms from two molecules, i dont want both of them to denoted by same atom type( say 1) in the lammps data file. Could you suggest how to solve the issue?
I guess this uses the built-in forcefield parameters, like CGenFF. I have created a parameter file using fftk tool kit. Is there any way to tell VMD to use my parameter file and make lammps data file using this? Please let me know if it is possible.
Hey, thank you very much, this video was very helpful. One question is whether this procedure was to create a single biomolecule, how can I put 100 molecules in a box of water, for example?
For this, first a molecule is modeled and then it is repeated as many times as desired in a simulation box using the Packmol software. This video will be released soon on the channel.
I did this with a pdb file generated from Avogadro. My molecule has a lot of double bonds C=C. It seems to me that the bond order is not being translated when I do this. Any tips?
Thank you so much. This is extremely helpful. I have a question though, why is it showing many atom types of the same atom ? for instance in the mass section, you can see the same atom considered as different types, although the mass is the same. Do i need to specify the potential between all atom types in LAMMPS ? Sorry if these questions are trivial, I am a beginner. Thanks again
You're welcome! These atoms, despite being the same, are chemically different from each other, and specific coefficients must be defined for each. See link below to read more: pubs.acs.org/doi/10.1021/j100389a010
Yes, you can use this method to get the data file for proteins with lammps format. Also, the following link has good information about various protein-based structures data files: lammpstube.com/2020/04/03/pdb-file-format/
It showing: ERROR) writelammpsdata: need to have non-zero box sizes to write a data file ERROR) writelammpsdata: current box sizes: {0.000000 0.000000 0.000000} -1 Can you please show me the way?
Another solution to that is you can put this line into the pdb file (you can open it with Notepad++) at the top row and it work for me but ım not sure if it will gone affect or change anything it works for me ım using this to make reaction molecule templates "CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1" (paste in without apostrophes)
1. Open PDB in any text editor 2. change the first three numbers from 0.0000 to 1.0000 3. save and close 4. restart vmd and load the edited pdb 5. input the command
For anyone having trouble with this error: ERROR) writelammpsdata: need to have non-zero box sizes to write a data file ERROR) writelammpsdata: current box sizes: {0.000000 0.000000 0.000000} You can put a line (given below) in the pdb file on toppest row and it works for me but ım not sure if its gone change anything ım using pdb files to make molecule templates for fix bond/react command ı have no problem using this way ı hope this helps "CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1" # paste it without apostrophes
you don't believe how precise this video was posted in terms of timing, my case though.
Wish you the very best.
Bro same... i was only getting the bonds and was so confused why it wasnt generating angles/dihedrals. saved my bacon after me searching for over 12 hours...
Thanks so much for this. The VMD user manual is not very intuitive for new users! You saved my grade!!!!
you are my savior
Hello, I am struggling with atom types of same element atoms which I need to denote differently in the Lammps data file from VMD. For example , in my pdb file there are 2 carbon atoms from two molecules, i dont want both of them to denoted by same atom type( say 1) in the lammps data file. Could you suggest how to solve the issue?
I guess this uses the built-in forcefield parameters, like CGenFF. I have created a parameter file using fftk tool kit. Is there any way to tell VMD to use my parameter file and make lammps data file using this? Please let me know if it is possible.
Hey, thank you very much, this video was very helpful. One question is whether this procedure was to create a single biomolecule, how can I put 100 molecules in a box of water, for example?
For this, first a molecule is modeled and then it is repeated as many times as desired in a simulation box using the Packmol software. This video will be released soon on the channel.
I did this with a pdb file generated from Avogadro. My molecule has a lot of double bonds C=C. It seems to me that the bond order is not being translated when I do this. Any tips?
I have given all the commands but at the end it shows as
"error, need to have non zero box size to write a data file"
could you please help.
Please use 1.9.2 version of VMD software ...
@@lammpstube is there anyway around this? i need to erase and redownload? ty.
@@devildog713Please use below link:
lammps.ir/VMD-windows64.exe
you could also try:
pbc set {X Y Z 0 0 0}
Where the X Y and Z are the dimensions of your box.
honestly, been getting the same error with ver. 1.9.4a55
Thank you so much
Thank you so much. This is extremely helpful. I have a question though, why is it showing many atom types of the same atom ? for instance in the mass section, you can see the same atom considered as different types, although the mass is the same.
Do i need to specify the potential between all atom types in LAMMPS ?
Sorry if these questions are trivial, I am a beginner.
Thanks again
You're welcome!
These atoms, despite being the same, are chemically different from each other, and specific coefficients must be defined for each. See link below to read more:
pubs.acs.org/doi/10.1021/j100389a010
@@lammpstube I'm unable to do this. Can you please guide me which softwares should we be having for this process?
Nice job
Thank you for this! Can Someone use this to get the data file for
proteins?
Yes, you can use this method to get the data file for
proteins with lammps format. Also, the following link has good information about various protein-based structures data files:
lammpstube.com/2020/04/03/pdb-file-format/
how to create semiconductors like Si and GaAs. please help
It showing:
ERROR) writelammpsdata: need to have non-zero box sizes to write a data file
ERROR) writelammpsdata: current box sizes: {0.000000 0.000000 0.000000}
-1
Can you please show me the way?
Please use 1.9.2 version of VMD software ...
Another solution to that is you can put this line into the pdb file (you can open it with Notepad++) at the top row and it work for me but ım not sure if it will gone affect or change anything it works for me ım using this to make reaction molecule templates
"CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1" (paste in without apostrophes)
1. Open PDB in any text editor
2. change the first three numbers from 0.0000 to 1.0000
3. save and close
4. restart vmd and load the edited pdb
5. input the command
How can i write pair_coefficient, angle_coefficient value in the data file?
There are good examples for these cases in LAMMPS manual:
docs.lammps.org/pair_coeff.html
docs.lammps.org/angle_coeff.html
@@lammpstube But those are the values! I mean for specific molecule for instance, benzene. where can i get those values in the data file?
@@anggonbarua4139 You can use various force-fields such as:
pubs.acs.org/doi/10.1021/j100389a010
pubs.acs.org/doi/10.1021/ja00051a040
...
Can vmd topotools write data with charge?
The best way to set atomic charge in data file is use "set/charge" command in LAMMPS script.
@@lammpstube thanks sir
@@sharmimazumder9502 Good luck!
its giving me the wrong values of xlo, xhi
As shown in video, these parameters must be modified manually by user in 1.9.2 version of VMD software.
For anyone having trouble with this error:
ERROR) writelammpsdata: need to have non-zero box sizes to write a data file
ERROR) writelammpsdata: current box sizes: {0.000000 0.000000 0.000000}
You can put a line (given below) in the pdb file on toppest row and it works for me but ım not sure if its gone change anything ım using pdb files to make molecule templates for fix bond/react command ı have no problem using this way ı hope this helps
"CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1" # paste it without apostrophes
lifesaver, thanks
0.000000 0.000000 xlo xhi
0.000000 0.000000 ylo yhi
0.000000 0.000000 zlo zhi
why ?
In old versions of VMD software (like VMD 1.9.2) the size of simulation box prints incorrectly and must be corrected manually.