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rmoltools & rmollib

What are rmoltools and rmollib? An example of rmollib being used in conjunction with gromacs. duration: 4 seconds. Is a C library written to manipulate molecules and systems of molecules stored in pdb, gro and pdbz files. It will give you access to molecules on the attomistic level, molecular level or the system level. The system can be edited in memory and then dumped to disk. It is meant for use with tool such as gromacs, Gaussian, and ToFeT. Remover a percentage of molecules from a simulation file.

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rmoltools & rmollib | rmollib.com Reviews

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What are rmoltools and rmollib? An example of rmollib being used in conjunction with gromacs. duration: 4 seconds. Is a C library written to manipulate molecules and systems of molecules stored in pdb, gro and pdbz files. It will give you access to molecules on the attomistic level, molecular level or the system level. The system can be edited in memory and then dumped to disk. It is meant for use with tool such as gromacs, Gaussian, and ToFeT. Remover a percentage of molecules from a simulation file.

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rmoltools & rmollib | rmollib.com Reviews

https://rmollib.com

What are rmoltools and rmollib? An example of rmollib being used in conjunction with gromacs. duration: 4 seconds. Is a C library written to manipulate molecules and systems of molecules stored in pdb, gro and pdbz files. It will give you access to molecules on the attomistic level, molecular level or the system level. The system can be edited in memory and then dumped to disk. It is meant for use with tool such as gromacs, Gaussian, and ToFeT. Remover a percentage of molecules from a simulation file.

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rmollib.com

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rmoltools & rmollib

http://www.rmollib.com/genbox.html

Generating random boxes of molecules (pdbgenbox). Generates a box filled with n copies of a molecule. Pdbgenbox - orig ./test.pdb - out ./out.pdb - random - mindist 2 - needed 120 - shift 2. Pdbgenbox - orig (input file pdb/gro) - out (output file pdb) - random - mindist (minimum interaction distance) - needed (number of copies) - shift (shift int). Bcb on a bcb lattice. Orig origonal input file. Shift shift the whole box. Random enable random placement. Mindist minimum separation distance of two atoms.

2

rmoltools & rmollib

http://www.rmollib.com/truncate.html

Truncate the velocities with in a gro file. When restarting crashed simulations it can be beneficial to truncate velocities so that the system state where the crash occurred is not reentered. This program will truncate the velocities. Pdbtruncate - in (filename .gro) - out (output file) - t (value to truncate by e.g. 0.00001). A truncated .gro file. Pdbtruncate - in in.gro - out out.gro - t 0.00001. Last updated Tue 07 Jul 2009 07:07:48 PM BST.

3

rmoltools & rmollib

http://www.rmollib.com/count.html

Count the number of one type of molecules in a file. Pdbcount - in (filename .gro/.pdb)- resid (molecule to count). Number of molecules in file. Out=`pdbcount - in one.gro - resid UNK`.

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rmoltools & rmollib

http://www.rmollib.com/stats.html

Provide useful statistics on a gro/pdb file. Rmoltools - stats (filename .gro/.pdb). Prints the total molecular mass of the pdb file. Prints the maximum/minimum x,y and z positions of atoms within the file. Pdbrod - stats one.gro.

5

rmoltools & rmollib

http://www.rmollib.com/evap.html

Removes a designated number of molecules from a simulation box. The result is dumped as a .gro file. Velocities are preserved. Pdbevap - in in.pdb - remove 0.70 - out out.gro - sol CCl. No evaperation (- remove 0.0). Remove 70% of the solvent (- remove 0.70). Remove 99% of the solvent (- remove 0.99). Pdbevap - in (input file) - remove (proportion of molecules to remove (0=none 1=all) - out (output file) - sol (name of the solvent to remove). Removes a designated number of molecules from a simulation box.

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Rmollib - C routines to manipulate gromacs. And pdb data files. A device model designed to simulate solar cells. Useful scientific data manipulation routines written in C. Download tar file i.tgz. Setting up a base system. If you are going to use this software and try to work with me it is probably best that you PC is to some extent configured the same a my systems. This is how to do that.

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rmoltools & rmollib

What are rmoltools and rmollib? An example of rmollib being used in conjunction with gromacs. duration: 4 seconds. Is a C library written to manipulate molecules and systems of molecules stored in pdb, gro and pdbz files. It will give you access to molecules on the attomistic level, molecular level or the system level. The system can be edited in memory and then dumped to disk. It is meant for use with tool such as gromacs, Gaussian, and ToFeT. Remover a percentage of molecules from a simulation file.

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