No MPI compilation.

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Please cite T. Matthey, T. Cickovski, S. S. Hampton, A. Ko, Q. Ma, M. Nyerges, T. Raeder,
T. Slabach, and J. A. Izaguirre. ProtoMol: An object-oriented framework for prototyping
novel algorithms for molecular dynamics. ACM Trans. Math. Softw., 30(3):237­265, 2004.
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ProtoMol Version 2.0.4

jesus Dec  4 2006 13:23:38
Linux localhost.localdomain 2.6.9-42.ELsmp #1 SMP Wed Jul 12 23:27:17 EDT 2006 i686 i686 i386 GNU/Linux
icpc -Wall -wd810,383,981,279,444,1572 -O3 -ip -DNDEBUG
32-bit
Intel(R) C++ Compiler for 32-bit applications, Version 8.1    Build 20060606Z Package ID: l_cc_pc_8.1.038
Copyright (C) 1985-2006 Intel Corporation.  All rights reserved.
Version 8.1 
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Information:

protomol@cse.nd.edu
http://protomol.sourceforge.net
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Integrators:
BBK
    timestep                       <real,positive>
    temperature                    <real,non-negative>
    gamma                          <real,non-negative>
    seed                           <int=1234,non-negative>
BSplineMOLLY
    cyclelength                    <int,positive>
    BSplineType                    <string=undefined,non-empty>	 # interpolation scheme (short | long)
    mollyStepsize                  <real,positive>
CGMinimizer
    timestep                       <real,positive>
    alpha                          <real=0.001,non-negative>	 # steplength 'sufficient decrease' parameter
    beta                           <real=0.05,non-negative>	 # steplength 'sufficient directional derivative reduction' parameter
    restart                        <real=0,non-negative>	 # steplength 'restart interval
DihedralHMC
    cyclelength                    <int,positive>
    temperature                    <real,non-negative>
    dihedralsSet                   <boolean=false>	 # If false a dihedral is selected randomly
    dhmcDiSetFile                  <string,non-empty>
    anglesSet                      <boolean=false>	 # If false the dihedral angle is selected randomly
    dhmcAnSetFile                  <string,non-empty>
DihedralLiftMC
    cyclelength                    <int,positive>
    temperature                    <real,non-negative>
DMDLeapfrog
    timestep                       <real,positive>
    iterations                     <int=2,non-negative>
    gamma                          <real,non-negative>
    temperature                    <real,non-negative>
    seed                           <int=1234,positive>
EquilibriumMOLLY
    cyclelength                    <int,positive>
hessianint
    timestep                       <real,positive>
    eigvecFile                     <string=>	 # Eigenvector filename
    eigvalFile                     <string=>	 # Eigenvalue filename
    hessianFile                    <string=>	 # Hessian sparse filename
    sortByAbs                      <boolean=false>	 # Sort eigenvalues/vectors by absolute magnitude
HybridMC
    cyclelength                    <int,positive>
    temperature                    <real,non-negative>
Impulse
    cyclelength                    <int,positive>
LangevinImpulse
    timestep                       <real,positive>
    temperature                    <real,non-negative>
    gamma                          <real,non-negative>
    seed                           <int=1234,non-negative>
Leapfrog
    timestep                       <real,positive>
NormModeInt
    cyclelength                    <int,positive>
    fixmodes                       <int=0,non-negative>	 # Number of high frequency modes constrained
    gamma                          <real=80,non-negative>	 # Langevin Gamma
    seed                           <int=1234,non-negative>	 # Langevin random seed
    temperature                    <real=300,non-negative>	 # Langevin temperature
    nve                            <int=0,non-negative>	 # NVE simulation if not 0
NormModeMin
    timestep                       <real,positive>
    minimlim                       <real=0.1,non-negative>	 # Minimizer target PE difference kcal mole^{-1}
NoseNVTLeapfrog
    timestep                       <real,positive>
    temperature                    <real=0,non-negative>	 # preferred system temperature
    thermal                        <real=0>	 # heat bath coupling: 1.0 very, very strong, 0.0 none
    bathPos                        <real=0>	 # history of the difference of system and heat bath
NPTVerlet
    timestep                       <real,positive>
    temperature                    <real=0>
    pressure                       <real=0>
    tauT                           <real=0>
    tauV                           <real=0>
    tauP                           <real=0>
PaulTrap
    timestep                       <real,positive>
    temperature                    <real=0,non-negative>
    thermal                        <real=0>
    bathPos                        <real=0>
    bathVel                        <real=1>
    scheme                         <string=NVT,non-empty>	 # thermostat scheme (NVT | NVT_zero | NVT_ind | NVT_shell | NVT_global | berendsen | berendsen_zero | berendsen_ind | berendsen_shell | berendsen_global)
    part                           <real=0,non-negative>
    time                           <vector=>
    t                              <vector=,non-negative>
PLeapfrog
    timestep                       <real,positive>
ShadowHMC
    cyclelength                    <int,positive>
    temperature                    <real,non-negative>
    order2k                        <uint=0>
    c                              <real=0>
    optimize                       <boolean=false>
    ratio                          <real=0>
Alias:
HBondMOLLY : BSplineMOLLY (BSplineMOLLY)
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