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[GROMACS tutorial](http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html )
[GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design](https://doi.org/10.1021/acs.jcim.2c0004…
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Our current harmonic angle oscillator has an option for `cos_angles` that we default to `True`. The original motivation for this was to avoid the numerical singularity that arises at 0 or 180 degrees.…
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Unclear what the "-DEQ_polyply" flag is, as mentioned at the end of section 4.
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### My Question is...
Does gmx_mmpbsa support GROMOS force fields? If not, what method can convert GROMOS force field files
kkivg updated
10 months ago
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Thank you for creating such a wonderful toolkit. Trying to build an all atomic block copolymer model for GROMACS. Thought it should be available with the '-connect' function with the gen_seq, but don'…
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GROMOS11 is a software to conduct molecular dynamics simulation. As of MDAnalysis version 2.6, GROMOS11 trajectories are not supported. To enable the research group I'm working with to use MDAnalysis,…
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I think it's getting to be time to start planning an 8.1 release. There've been a number of important changes added since 8.0, including a bunch of performance improvements, ATMForce, and support for…
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### Steps to reproduce the issue
```console
$ spack spec -I cp2k+cosma+libvori+mpi_f08+pexsi+plumed+pytorch+quip+sirius+spglib+ipo+elpa+dlaf+openmp build_system=cmake lmax=7 ^cosma+shared ^cmake/v…
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I'm trying to run a simulation using gromacs topology and coordinate files. When I try to load the topology file I get the following error:
.....
File "gromacstopfile.py", line 247, in _process…
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I am trying to convert gromacs topology file to amber topology file to used MMPBSA or MMGBSA module of Amber Tool.
For this I used the following command
**parmed -p topol.top -O amb.parm7**
After r…