Subject: a MD rookie's startup difficulties

From: root <[email-masked]>
Date: Sun, 30 Nov 1997 21:14:33 +0300 (MSK)

Dear CCLers,

I've just recently started digging into this exciting field: computer
modelling of large (bio)macromolecular system dynamics. Naturally, I am
running into initial difficulties I am unable to resolve on my own. Since
there are no MD wizards in my vicinity, I've decided to turn to the CCL
list, which has in the past always been very helpful. 

Here's what I am trying to do: to study polycation-induced lateral
segregation of lipid anions in lipid bilayers (actually, I'd like to do
polycation-induced flip-flop, but that's pure SF just now) by means of
molecular dynamics. (I can't dig Monte Carlo very well, and it seems to
produce lots of artefacts, especially on lattices). 

Initially, I was thinking to start with the following system caricature: 
approximating the linear polycation by an linearly linked but otherwise
unconstrained chain of Lennard-Jones balls, some of which are charged
hovering in vacuum over an 2d array of LJ balls (some of them charged,
either in a random distribution, or in contiguous blocks to mimick block
copolymers) constrained in the z direction by a narrow parabolic potential
well. Their movements are dampened in the xy plane. System's periodic
boundary condition is suspended in the z direction. Both components are
allowed to relaxate in isolation. The polycation should resemble a
self-avoiding random walk with additional electrostatic repulsion. The
same electrostatic repulsion should generate a roughly hexagonal ion
pattern embedded into the neutral ball matrix. 

Alas, I soon realized existing packages offer no easy support for setting
up such simple systems. Rolling one's own by modifying e.g. D.C.
Rapaport's code form "The Art of Molecular Dynamics Simulation" was out of
question due to lack of time. 

So I decided to skip this first step, progressing immediately to a
physically realistic system which, paradoxically, seemed easier. While
searching for free packages which, also, ran on Linux, I encountered
VMD/NAMD, which seemed to offer the most advanced features. I found their
advertised features as good scalability, capability to render
publication-quality images, remote realtime visualization and realtime
control of the running system (as introduction of perturbative forces) 
particularly appealing.

Though so far I have been unable to compile NAMD under Linux and getting
my binary tarball of VMD to work on my RedHat 4.2 Linux box, I got NAMD to
work in single-node mode (built PVM, also, does not work quite right yet,
but I'm working on it) under IRIX 5.3 on an SGI Indy. Another difficulty
emerged: while I have been able to generate good *.pdb structures of
polymers (so far only polyvinylpyrrolidone oligomers) with Gasteiger's
CORINA email facility from manually constructed SMILES strings (is there
an easier way?), I had no such luck with the according *.psf file. NAMD
manual says they can be fashioned with XPLOR (which I do not have), or by
hand. Since my system will get pretty large finally, I'd rather avoid the
latter option. Is there another alternative I failed to notice? 

Since protein polycations tend to be rather stiff, and interesting effects
start to occur only beyond the molecule segment's length, I'd rather avoid
them. My ad hoc system of choice is a random vinylpyrrolidone/vinylamin
copolymer.  Does anybody study (nonrigid and/or solvated) polymeric
polycations here?

Finally, I'd like to inquire whether, and where, can one obtain simulation
boxes with well-equilibrated hydrated lipid (bi/mono)layer patches,
preferably with a fraction of the membrane lipids negatively charged. 

Thanks a lot,
Eugene Leitl, MSU, Polymer Science Dept.