#30054 - 05/28/12 05:54 PM
READ BEFORE POSTING; updated March 2016
Loc: 39 03 48 N, 77 06 54 W
NoticesThe charmm.org site has been updated (March 2016), and has a revised layout running on new hardware. The forums do not appear to be unduly impacted; however, the new layout does mean that bookmarks and links to the documentation will need to be changed. For searches with Bing, Google, Yahoo, etc., use the site: operator; see the miniFAQ below.
A notable new item is the availability of charmm, a free version of CHARMM, but w/o any of the newer high performance features; registration is required. See the miniFAQ below, or the main CHARMM site page. Guidelines for postingGeneral
CHARMM is a research tool intended mainly for a graduate student level and above user base, with the appropriate background in biochemistry, physical chemistry, mathematics, and computational methods. These forums are intended to assist such people with usage of the CHARMM program, and cannot replace mentors with skills in those fields. Many of the scientists who answer questions on these forums are busy professionals, who don't have a lot of spare time. It may take a couple days for the right person to read your question and respond; please be patient. Choose an appropriate forum and Subject
line for your question, and before posting, take the time to properly research your question (documentation, forum or other online searches, people in your lab, etc.). Be specific in your post, and indicate what steps you have taken to try to resolve the problem; provide some detail, but avoid overly long data dumps. More specific guidelines are given below; some common general questions are answered in the miniFAQ
at the end of this post.Also, the usual rules apply: obscenity, profanity, personal attacks, ads, spam, phishing links, and other types of anti-social behavior are strictly prohibited. While not formally moderated (posts are not reviewed before appearing), the posts are monitored regularly, and the forum admins reserve the right to delete posts and ban users for bad behavior.
Finally, some questions may not be answered because those with expertise in the area are not regular contributors to these forums; participation here is voluntary, and the user may sometimes need to contact code or publication authors directly. It should be noted that CHARMM has been in use for over 25 years, and some of the code may no longer be actively supported by any of the current developers. As of the c36b1 release, some legacy features were removed from the code during the conversion to Fortran95.Specifics
- Choose the appropriate forum (see below); do not post the same question in multiple forums. The forum admins may move your post to another forum, and they will also delete duplicated posts.
- Prior to posting, read some posts in the chosen forum, esp. any "sticky" posts at the top of the main forum page; note what kinds of questions get serious and respectful answers. Research your question further using the built-in forum search or the site: operator with search engines (see the miniFAQ below).
- For a new question, use the New Topic button on the main page of each forum; do not reply to a marginally related post just because one of the error messages is the same. Be sure to use descriptive and specific text for the Subject field.
- When posting anything other than a quick reply, using the Switch to Full Reply Screen button is highly encouraged (and required for attachments).
- Include relevant details, esp. the hardware platform, CHARMM version, compiler and version, and the operating system and version.
- Posting of input scripts is encouraged, but longer scripts should be attached (via Full Reply Screen), after adding a .txt file extension (best for viewing via web browsers). For problems with scripts generated by web sites, consider contacting the people running the web site; for CHARMMing or CHARMM-GUI, use one of those specific forums.
- To preserve whitespace in posts, use the [ code] ... [/code] markup tag, which is also accessible via a drop down menu from the '#' symbol on the Full Reply Screen. (Note: There should be no spaces inside the  tag, or it will simply be displayed, as shown here; see the UBBcode topic in the bulletin board FAQ.)
- CHARMM output may be included, but should be attached, renamed by adding a .txt extension; larger files should be edited to remove redundant messages or data listings. Always include the first part of the output file, esp. any warning messages during the setup phase of the calculation. (The final failure and the lines just before it are not always sufficient to diagnose a problem; setup errors can be the ultimate cause.)
- DO NOT ask for help with scripts run with a BOMLEV less than -1; it's usually a waste of everyone's time. Most scripts can be run with BOMLEV 0; errors should be fixed, not suppressed.
- Because of the great diversity of forum users, try to write complete English sentences, and avoid the use of slang or texting abbreviations.
Too many people simply post in the first forum, rather than the best one; please try to do better. A new post with a descriptive Subject in the best forum for the topic or question may get answered sooner, and helps keep the information here organized; also, a number of the experts only monitor specific forums.
Some tips for making a choice within the User Discussion & Questions
- Setup, I/O, and Basic questions
Writing CHARMM input scripts, reading and writing data files, and fundamental CHARMM usage issues should be addressed here. (There are other forums for questions about adding molecules, specifying energy terms, running dynamics, analyzing trajectories, compiling CHARMM, etc.)
- Energy terms, Constraints, Restraints, and Solvation
Non-bond specifications, when and how to use SHAKE, how to add restraint forces, implicit solvent models, interaction energy, energy analysis, etc.
- Parameter Set Discussion
Existing topology and parameter files, their format and contents, and how to add new molecules.
- Molecular Dynamics
Running dynamics (MD, LD), boundary conditions, statistical mechanics ensembles, analyzing the trajectories
- Minimization, Normal modes, Monte Carlo,...
Choice and usage of minimization methods, using VIBRAN for calculating vibrational normal modes, Monte Carlo sampling
- Installation and Testing
Compiling CHARMM, adding features (esp. parallel MPI), running the testcases, etc.
- Performance and Benchmarking
Improving and testing program performance; using the new DOMDEC (domain decompostion) and OpenMM, faster FFT for PM Ewald, LOOKUP tables, reducing list updates, etc.
- Other User Discussion and Questions
Some of the CHARMM related questions in the first "Setup, I/O, ..." forum probably belong here, or in one of the other above forums.
- General Chemistry Discussions
More general computational chemistry topics, not specifically about CHARMM, should be posted in this forum.
For the CHARMM Interfaces
miniFAQ Where can I download CHARMM?
- QM/MM Discussion and Questions
QM/MM interfaces, both semi-empirical and ab initio methods
support for the CHARMMing web site
support for the CHARMM-GUI web site
support for using CHARMM with MMTSB (Multiscale Modeling Tools for Structural Biology)
the commercial provider, repackaged as CHARMm
Starting with c40b2, there is a version with no fee, denoted charmm
, which can be downloaded after registration by researchers in non-commercial organizations. The full version, denoted CHARMM
, still requires the (modest) academic license fee and includes additional performance features, notably the domain decomposition (DOMDEC) method, including a GPU-based non-bond engine. For either charmm or CHARMM, see this page
.  How can I search the forums and documentation?
The charmm.org and forum search features are fairly limited, so one way to get better search results is to use the site: operator with any of the major Internet search engines, e.g. in a Google search text field enternoe site:www.charmm.org
The first example searches the full site, the second searches just the forums, and the third searches the documentation for c40b1 only. What is required to install CHARMM?
A fairly up to date Linux system with a tcsh shell and a complete development environment, including make and both C and Fortran compilers installed; see install.doc for more Fortran compiler information. For added features such as parallel, graphics, ab initio
QM, OpenMM, etc., other libraries or programs may be needed, and many cannot be re-distributed due to their license; they must be obtained and installed independently. See the appropriate CHARMM .doc file describing the feature for information on external library or program requirements.
READ BEFORE POSTING; updated March 2016
05/28/12 05:54 PM