1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
|
<!DOCTYPE HTML PUBLIC "-//W3O//DTD W3 HTML 2.0//EN">
<!Converted with LaTeX2HTML 95.1 (Fri Jan 20 1995) by Nikos Drakos (nikos@cbl.leeds.ac.uk), CBLU, University of Leeds >
<HR>
<CENTER>
<A href="t0_l.gif"><IMG ALIGN=MIDDLE ALT=" " SRC="t0_ss.gif"></A>
<IMG ALIGN=MIDDLE ALT=" " SRC="solvate.gif">
<A href="t8_l.gif"><IMG ALIGN=MIDDLE ALT=" " SRC="t8_ss.gif"></A><BR>
</CENTER>
<HR>
<HEAD>
<TITLE> Purpose</TITLE>
</HEAD>
<BODY>
<meta name="description" value=" Purpose">
<meta name="keywords" value="docu">
<meta name="resource-type" value="document">
<meta name="distribution" value="global">
<P>
<H1><A NAME=SECTION00030000000000000000> Purpose</A></H1>
<P>
Molecular dynamics (MD) studies of biological macromolecules
(such as proteins or DNA) require a large amount
of computations, mainly due to the large number of atoms
(typically several thousands) such molecules consist of.
Even when using supercomputers, this computational complexity
limits such simulations to very short
time scales, typically a few nanoseconds.
<P>
Furthermore, just considering the macromolecule of interest
is not enough, for the physiological environment of the
molecule (e.g., for globular proteins, water solvent and salt ions)
strongly interacts with the dissolved macromolecule. Therefore,
also part of that environment has to be included within the simulation
system, which then usually contains several tens of thousands of
atoms [<A HREF="node6.html#Heller93a">1</A>,<A HREF="node6.html#Grubmuller95b">2</A>].
Obviously, one wishes to include only as many solvent molecules
within the simulation system as <em> really</em> necessary, while
keeping the influence of the (artificial) system boundary (the surface
of the solvent) onto the dissolved macromolecule as small as
possible. <tt> SOLVATE</tt> serves this purpose.
<P>
<tt> SOLVATE</tt> is a program to construct an atomic model
of a solvent environment for a given atomic macromolecule model
(solute). Its main feature is that it can create <em> irregularly</em>-shaped
solvent volumes specifically adapted to the (mostly also irregular)
shape of the solute. As a result, the number of atoms
that have to be considered in the MD-simulation is significantly
reduced in comparison to the usual box- or sphere-shaped
volumes, so that the simulations run considerably faster.
<P>
<tt> SOLVATE</tt> accepts pdb-files (Brookhaven Data Bank/X-PLOR format)
of the solute as input; the output
is a pdb-file of the solute plus a number of water molecules and,
optionally, sodium and chloride ions placed in accordance with a
Debye-Hückel-distribution. To generate ions, an
X-PLOR protein structure (psf-)file of the solute (which contains
the partial charges of the solute atoms) is
required in addition to the pdb-file.
An X-PLOR-script to create a protein structure file of the
solute/water/ion-system can be generated.
Note that the output structure is <em> not</em> equilibrated,
since this can be done with the usual programs, e.g., CHARMm [<A HREF="node6.html#Brooks83">3</A>],
X-PLOR [<A HREF="node6.html#XPLOR">4</A>], or
<A NAME=tex2html6 HREF="http://www.imo.physik.uni-muenchen.de/ego.html">EGO</A> [<A HREF="node6.html#Eichinger95b">5</A>].
<P>
Clearly, just creating solute-adapted solvent volumes is not an art ---
it can easily be done, e.g., with the <tt> around</tt>-function of X-PLOR.
However, just to have such a solvent/solute-system is not
enough for an MD-simulation. Rather, water molecules near the surface
of the solvent volume must be subjected to
`boundary-forces' in order
to prevent these water molecules from evaporating into the vacuum.
Ideally, these forces should substitute all those forces (e.g., electrostatic
interactions and van der Waals contacts), which would originate from
solvent molecules <em> outside</em> the simulation system.
The socalled `stochastic boundary'-approach [<A HREF="node6.html#Brooks83a">6</A>,<A HREF="node6.html#Bruenger85">7</A>] provides
such forces in a simple approximation by use of a suitable
boundary potential.
<P>
Such boundary potentials are generally functions of the distance
between the particle, onto which the force acts, and
the boundary of the simulation system. Hence, for an efficient
computation of the forces derived from this potential, it should be
of simple analytic form. This is the reason why, typically, box-
or sphere-shaped solvent-volumes are used.
<P>
<tt> SOLVATE</tt> provides an (almost) arbitrarily-shaped solvent volume
<em> and</em> a simple analytic description of its boundary using
few multivariate gaussian functions. That choice of description
enables efficient computation of distances
between water molecules and the boundary
during subsequent MD-simulations. The necessary algorithms will soon be
implemented into the MD-program
<A NAME=tex2html7 HREF="http://www.imo.physik.uni-muenchen.de/ego.html">EGO</A>,
but they can
also easily be implemented within CHARMm or X-PLOR.
<P>
<BR> <HR>
<P><ADDRESS>
<I>Helmut Grubmueller <BR>
Wed Jun 19 19:00:00 MET DST 1996</I>
</ADDRESS>
</BODY>
|
