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Mark J. Williamson

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Mark J. Williamson created

Please see the link: http://ambermd.org/formats.html#parm.dat This explains the format used in the file. With respect to the terms that you describe as "duplicate atom groups with different params", a single given torsion parameter can be synthesised from multiple cosine terms ( see p259 of http://ambermd.org/doc8/amber8.pdf ) and the use of the negative PN value is an indication NOTE: If PN .lt. 0.0 then the torsional potential is assumed to have more than one term, and the values of the rest of the terms are read from the next cards until a positive PN is encountered. The negative value of pn is used only for identifying the existence of the next term and only the absolute value of PN is kept.

Mark J. Williamson updated

Please see the link: http://ambermd.org/formats.html#parm.dat This explains the format used in the file. With respect to the terms that you describe as "duplicate atom groups with different params", a single given torsion parameter can be synthesised from multiple cosine terms ( see p259 of http://ambermd.org/doc8/amber8.pdf ) and the use of the negative PN value is an indication NOTE: If PN .lt. 0.0 then the torsional potential is assumed to have more than one term, and the values of the rest of the terms are read from the next cards until a positive PN is encountered. The negative value of pn is used only for identifying the existence of the next term and only the absolute value of PN is kept.

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