In case it's relevant, my data file was put together in VMD 1.9.1 with topotools, using the command, If anyone can spot my mistake, I'd greatly appreciate the help. I hope I'm not missing something obvious here, but I'm a little baffled. They also include the charges section, and I completed the tutorials without any issue. I compared my input files to those used in the second part of the tutorials. Kohlmeyer's tutorials to help me do this. I just can't figure out why the format is wrong when I try to include them. This makes sense - of course the charges are required to compute coulombic forces. Obviously, this is a result of a command in my input file: In its place, I get another error: "Pair style lj/cut/coul/dsf requires atom attribute q (./pair_lj_cut_coul_dsf.cpp:266)". However, if I eliminate the charges column, the error goes away. I can "fix" one, but the fix causes the other and vice versa. I have searched for my error, but could not find anybody who had the same problem.
The newly available automatic conversion capability breaks down barriers between simulation tools and user communities and allows users to easily compare simulation programs and leverage their unique features without the tedium of constructing a topology twice.I am using the 12 April 2013 version of LAMMPS.
By applying the conversion process to conventional benchmark systems that mimic typical modestly sized MD systems, we explore the effect of the implementation choices made in CHARMM, NAMD, and GROMACS. The resulting comparison between energy terms shows that the translation performed was lossless as the energies were unchanged for identical starting configurations. The conversion process was diligently tested on a comprehensive set of biological molecules in vacuo.
#VMD TOPOTOOLS SOFTWARE#
We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within the widely used molecular visualization and analysis software VMD. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input.
These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology.
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