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Setup, I/O, and Basic questions
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Hi, I am a beginner in charmm. I looked through the io.doc, scalar.doc, however I couldn't figure this out. I used the following command. scalar wmain show sele type ca end I know that the result shows in the output file. My question is how I can
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Minimization, Normal modes, Monte Carlo,...
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The output log file from the minimization should give some hints, esp. if the problem is related to one of the energy terms. Note that VIBRAN does not support SHAKE, EWALD, or periodic boundaries, so you should not use them for the minimization. Ju
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Energy terms, Constraints, Restraints, and Solvation
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I know nothing about hqbm, but general advice is to show actual commands (and relevant output) instead of description of commands
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CHARMMing
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All, www.charmming.org is back on-line and running the brand version 0.8 of the CHARMMing software! There is a note on the front page describing some of the new features of this version. I am sorry about the extended downtime. Version 0.8 is still
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Parameter Set Discussion
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I'm sorry if I was unclear. What part did you not understand?
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Parameter Set Discussion
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Some of the permutations would require a different force constant, others not. Bottom line is that it's not safe to change the order of the atoms in the parameter file. Instead, it's better to just make sure that the order of the atoms in the topolog
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Parameter Set Discussion
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Didn't Alex release the new CHARMM force fields yet? We reorganized all the files (including heme) so that they use FLEX. I'm currently traveling but I will look into it when I can.
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Parameter Set Discussion
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I don't understand your question. It's "consequence 2" in that FAQ entry - the "CG2R61 CG2R61 CG301 CG331" should only have a 6-fold term. This term is not present in butylbenzene, hence you cannot use butylbenzene parameters. Rat
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Parameter Set Discussion
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And was the structure in the end similar to the experimentally obtained structure?
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Installation and Performance
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I had the same problem (seg. fault at every HEAP expansion) I was able to get a working exe by forcing it to compile in a 32bit mode (w. -m32 compiler flag).
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Energy terms, Constraints, Restraints, and Solvation
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From the summary of the nonbond and image data structures, I can see that: - The total number of interactions (NNNB) is not the same in two replicas. I dont see how this is possible since the vdw and coulomb terms are the same - The size of the JN
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Setup, I/O, and Basic questions
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1/ You open a file which seems (from its name and title) to be an RTF, then you read it as if it were a parameter file (and vice versa). 2/ The error message indicates that you have not followed the format for an RTF (or parameter file) 3/ If you rea
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Molecular Dynamics
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According to phmd.doc, the titratable groups are user specified.
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Energy terms, Constraints, Restraints, and Solvation
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What do you mean when you say that you gave "QECONT .eq. 0"? You should normally give values to EU, and the derivatives of your energy function to DX,DY,DZ. If your energy function is E=(X,Y,Z), then you get (DX,DY,DZ) = grad(E(X,Y,Z)) ie,
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Parameter Set Discussion
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I would have told you if I did...
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Parameter Set Discussion
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Just FYI, there's yet another urea model in CGenFF. I believe Alex put it together (but don't take my word for it). It might be interesting to test it along with the others.
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Parameter Set Discussion
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Originally Posted By: tianjThis is the same as what it is in Amber force field. That's an outrage! We have to change the CHARMM combing rules! Perhaps we might use these ones for the CHARMM Drude Polarizable FF: C. Baker et al., J. Chem. Theory Co
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