Various questions

From: Douglas Houston (
Date: Tue Jan 21 2014 - 09:42:14 CST

Dear all,

I am a beginner when it comes to NAMD but have been working through
the helpful tutorials. However, I have a few questions that I have not
been able to find the answers to:

1. The NAMD tutorial includes an example of a simulation in a sphere
with non-periodic boundary conditions. Why do I only ever read about
simulating in a box with periodic boundary conditions in the
literature? Maybe I'm just not reading enough ;-) but is there a
discussion of the pros and cons of each anywhere?

2. I have used mainly Gromacs in the past - Gromacs automatically
detects and applies its equivalents of NAMD's Cellorigin and
BasisVector 1, 2 and 3 keywords. Is there a way to get NAMD to do this?

3. From the NAMD tutorial: "One typically minimizes the system and
then equilibrates with the atoms in the protein fixed in space." But
there is no mention of this in the example .conf file that is
provided. What are the keywords relevant for fixing solute? Does
anyone have an example .conf file of a "standard" protein relaxation
protocol? I have seen example protocols for Gromacs and Desmond but is
there a "default" one for NAMD?

4. I have been working on generating a .psf for an olefin stapled
peptide. I have added an entry to the CHARMM parameter file and got
psfgen to output a .psf that looks OK in VMD (by OK I mean that the
right bonds are visible and hydrogen addition looks sensible).
However, I'm worried there may be some BOND, DIHE, IMPR or other
inappropriate descriptions I've missed (for example, I've used patches
to connect the linker to the backbone, which necessitated deleting the
existing backbone peptide bonds - but have I deleted everything I
should have?). I understand a validation run might identify incorrect
atomic motions but before that is there a way to visualise all entries
in the .psf file using VMD (or should I direct this to the VMD mailing

5. Related to 4., are entries like IMPR disregarded if there is not a
corresponding BOND? If so that would make me less worried about
catching every single one.

6. Why are the hexene methanediyl hydrogens in the
top_all27_prot_lipid.inp file a different atom type (HAL2) than e.g.
lysine side chain methanediyl hydrogens (i.e. HA)? I note the charges
are the same. The olefin staple is essentially a monounsaturated lipid
and I've built it using -CH2 parameters taken from amino acid side
chains but the hexene parameters seem equally correct to me. What's
the difference between these atom types?

7. I think that's enough questions for now!

Many thanks for any advice.



Dr. Douglas R. Houston
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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