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I plan to use CMAP terms in a MD simulation, I know that both top_all22_prot_cmap.inp and par_all22_prot_cmap.inp should be used, but besides them, is it necessary to explicitly specify "CMAP" somewhere in the input charmm script? Thanks in advance.

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Reading the RTF/PARAM files with the CMAP definitions is sufficient, provided the CHARMM release is recent enough. I believe CMAP is included as a standard feature for c31b1 and later, and may be available as an optional feature (recompile required) for c30 versions.


Rick Venable
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Thank you very much for your fast reply.
I recently perofrmed some MD simulations for ace-ala-nme in tip3 water, I did read the RTF/PARAM files with the CMAP definitions, but for the all 5ns simulation started from different initial conformation of ala2, the results of fi-psi angle population are consistent to the PAR22 result, but not the CMAP result. That is why I would like to ask the above question.

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Here are one of my results, starting from same initial conformation of ALA2, but at different temperature, the left panel corresponds to T=300K, and the right panel corresponds to T=600K. They are typical PAR22 rather than CMAP field results.

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The CMAP terms are defined in a general way, e.g.

CMAP -C N CA C N CA C +N

The above doesn't apply at chain ends, however, as the atom names for the acetyl carbon and methylamine N are different. There is a custom residue for the alanine dipeptide, ALAD, which has the CMAP terms applied properly for this somewhat pathological case. There are comments in the topology file that indicate this.


Rick Venable
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Aha!, yes. I got the point. Thank you very much.

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if CMAP is being used an additional line, 'CROSS>' in the energy section of the output file will be present.

alex


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Hi , is it possible to enumarte the cmap in a given system ?

the information is it profited by "print ic "?


regard david

Last edited by D.A; 08/05/22 08:43 AM.
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PRINT PSF or PRINT PARAM USED may be useful for this


Rick Venable
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