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如果用CHARMM GUI生成的输入文件没有READ ME文件怎么办?
![image](https://user-images.githubusercontent.com/89883577/203975008-93e8bb47-e315-4555-ad04-1e68cf53cbc9.png)
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***(1)*** Where can i find documentation for what CHL1, ASM, LSM, BSM, BENA, ... are in spica_top.json ? Some of them can be seen at https://www.spica-ff.org/forcefield.html but i cant find anythin…
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i have and str and mol2 files, but i dont know how can i convert charmm-cgenff force field to gromacs.
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I'm just going to keep track of what needs to be done in LAMMPS here so if anyone who feels the desire to chip in on something knows where to look.
- The hyperlinks are to the LAMMPS documentation f…
ctk3b updated
5 years ago
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It seems the martinze2 cannot recognize the DNA.
The error is
WARNING - unknown-residue - Can't add bonds based on atom names for residue A-DT1 because 'Residue DT is not known to force field charm…
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charmm interface FF from charmm-gui
the rtf like this:
> * INTERFACE FF
> * topology for nanomaterials
> *
> 36 1
the prm title:
> * INTERFACE FF
> * topology and parameter for caly m…
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Hi,
Is it possible to use another force field for small molecules like OpenFF? or is it hard to try to implement that?
Is it use Single or Dual topology for the openMM option? Is it possible to …
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I am planning to create a MolecularSystem class inheriting from BaseSystem. Its purpose will be to:
- Act as a superclass for AMBERSystem and any future CHARMM, GROMOS etc. style systems;
- Identify t…
khs26 updated
11 years ago
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Hi,
I'm running simulation starting form CHARMM-style force field, and trying to add an custom nonbonded force which is
```
f1 = f"""(ke/er*charge1*charge2)/r*exp(-r*kf)"""
or
f2 = f"""(ke/20*c…
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I tried using the ffID flag to change the charge set to CHARMM (`'ffID' : 'CHARMM36m'`). After I did this the console print out just showed `Start Preprocessing` for each of the input PDBs and did no…