This is a set of programs to perform coarse-grained MD simulations described in 
"Heat conductivity of the DNA double helix", by AV Savin, MA MAzo, IP Kikot, LI Manevitc, and AV Onufriev. Submitted to Phys. Rev. B.  

Below is the list of programs  and their brief descriptions. 
See Examples/ directory for more details and examples.

AUTHORS: A.V.Savin, I.P.Kikot, M.A.Mazo
TERMS OF USE: free.

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PROGRAM namb.f
Simulation of dynamics of DNA double-helix with use amber base-base potentials
Input:
"namb.crd" - the file where start coordinates and velocities
             of all particles are recorded (this file can be
             generated by minimization program or can be result
             of previous simulations)
"svblk" - file for random number generating
"namb.nam" - file with common parameters:
DT - integration time step (in ps)
NDT - number of DT steps in "large step" (usually NDT*DT=1ps)
NG - number of "large steps" in the simulation
NGT - each ngt "large steps" the coordinates are recorded
      in trajectory file "namb.trj"
INT=1 - Langevin thermostat on
INT=0 - Langevin thermostat off
TR - relaxation time of Langevin thermostat
TMP - temperature of Langevin thermostat
IRAND= 0/1  - method of random number generating (see RAND.F)
IMT=1/2 - method of numerical integrating (1 - Runge-Kutt, 2 - Verlet)
"namb.prm" - parameters of the potential function

Output:
"namb.pdb" - pdb-file of the last frame
"namb_.pdb" - pdb-file of the last frame with all-atom
              representation of nitrogen bases
"namb_r_order.pdb" - pdb file of the first frame in which
                     the order of the particles is the same as
                     in the program and trj-file
"namb.trj" - trajectory file where coordinates are recorded
             every NGT "large steps". The format of the file
             is the same as as in the "AMBER coordinate file".
"svblk" - file for random number generating
"namb.crd" - the file where coordinates and velocities of
             all particles are output when the simulation is finished.
Description:
the program gets coordinates and velocities from file "namb.crd"
and simulates molecular dynamics of the system. The user can use
pdb-files for investigating the behaviour of the system while
simulating. When the run is completed, all frames are written
in the namb.trj file. This file can be used for analysis of
dynamics and also it can be loaded into VMD program
(with namb_r_order.pdb file) to visualize the dynamics.
link in INTEL FORTRAN
Windows:
ifort -O namb.f rand.f
Linux:
ifort -O -o namb.x namb.f rand.f


PROGRAM famb.f
Find of the ground state of the DNA double-helix. Uses of amber base-base
potentials. Conjugated gradient method (program conmin.f) is used.
Input:
"famb.prm" - file for parameters of potentials
             and common parameters
"famb.nam" - file with base pair sequence
N - number of base pairs
NCONMIN - number of subroutine CONMIN runs (usually NCONMIN=10)
IB(I,1) - defines base sequence on the first strand
IB(I,2) - defines base sequence on the second strand
          IB=1,2,3,4 for bases A,T,G,C
Output:
"famb.pdb" - pdb file of the ground state of double-helix
             (only for grains of coarse-grained model)
"famb_.pdb" - pdb file of the ground state of double-helix
              (with all atomic representation of nitrogen bases )
"famb.crd" - coordinate file of the ground state of double-helix
             (can be used as start point in DNA molecular dynamics
              simulation by namb.f program)
link in INTEL FORTRAN
Windows:
ifort -O famb.f conmin.f
Linux:
ifort -O -o famb.x famb.f conmin.f


PROGRAM kamb.f
Finds ground state of finite homogeneous DNA poly(C)-poly(G)
double-helix. Uses amber base-base potentials.
The method of conjugate gradients (fmcg.f program) is used.
Input:
"kamb.prm" - file for parameters of potentials
             and common parameters, N is base pair number
Output:
"kamb.pdb" - pdb file of the ground state of double-helix
             (only grains of coarse-grained model)
"kamb_.pdb" - pdb file of the ground state of double-helix
              (with all-atomic representation of nitrogen bases)
"kamb.int" - coordinate file of the ground state of double-helix
             (can be used for creating a start point for thermal
              conductivity simulating by tamb.f program)
"kamb.crd" - coordinate file of one site of the ground state of
             DNA poly(C)-poly(G) double-helix + twist and
             rise parameters
link in INTEL FORTRAN
Windows:
ifort -O kamb.f fmcg.f
Linux:
ifort -O -o kamb.x kamb.f fmcg.f


PROGRAM tamb.f
Simulation of heat conductivity of finite homogeneous DNA (CG)_n
double-helix. Uses amber base-base potentials (mpi version)
Input:
"tamb.prm" - file for parameters of potentials
             and common parameters
DT - integration time  step (in ps) (typical value 0.0005ps)
NDT - number of DT steps in "big step" (typical value 20000)
MM - number of "big steps" in "large step"  (typical value 10)
NG - number of "large steps" in the simulation
IRAND= 0/1  - method of random number generating (see RAND.F)
IMT=1/2 - numerical integration method
          (1 - Runge-Kutt, 2 - Verlet)
Input and Output:
"svblk" - file for random number generating
"tamb.crd" - the file where coordinates and velocities of
             all particles after are written once the simulation is finished.
N - base pairs number
ING - number of the large step corresponding to the current
      coordinate set (for the initial point ING=0)
T - current time value (for the initial point T=0)
NT - number of end base pairs which are in Langevin's thermostate
TMP1 - thermostat temperature on the left end
TMP2 - thermostat temperature on the right end
TR - relaxation time of Langevin thermostate
Output:
"tamb.rez" - a file in which simulation results are saved
             (distribution of temperature and thermul flux
              along the double helix)
"tamb.tmp" - file with last large step simulation results 
"tamb.pdb" - pdb-file of the last frame
link in MPI FORTRAN
mpif77 -O -o tamb.x tamb.f rand.f
