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#8434 - 10/05/05 11:17 AM Need example files for DNA with water and ions
suresh Offline
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Registered: 01/18/05
Posts: 10
We are interested in an example input file/files for simulation of DNA with explicit water and ions. Is such an example available?


Edited by suresh (10/05/05 11:19 AM)

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#8435 - 10/05/05 12:12 PM Re: Need example files for DNA with water and ions [Re: suresh]
lennart Online   content

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Registered: 09/25/03
Posts: 4742
Loc: ~ 59N, 15E
You can easily combine files in the Script Archive to achieve this (gen-dna + run*md are good starting points).
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#8436 - 10/05/05 12:52 PM Re: Need example files for DNA with water and ions [Re: lennart]
rmv Online   content

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Registered: 09/17/03
Posts: 8379
Loc: 39 03 48 N, 77 06 54 W
Note, however, that the run-cpt-md.inp example suggests the use of an ORTHorhombic lattice with CPT dynamics, a practice I do not recommend; there are known examples where changes in the box shape (collapse of one of the edge lengths) have caused problems. Instead, shapes with isotropic symmetry should probably be used, such as CUBIC, RHDO, or OCTA; the latter 2 are more spherical in shape, and typically require less solvent than CUBIC.
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Rick Venable
computational chemist


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