public static void SelfTest(string rootpath, string[] args)
{
if (selftest == false)
{
return;
}
selftest = false;
string filepath = rootpath + @"\Bioinfo\External.Gromacs\Selftest\FileTrajectory.traj.txt";
FileTrajectory eigvec = FromFile(filepath);
}
public static FileTrajectory FromLines(string[] lines)
{
List <List <string> > frameliness = GroupByFrames(lines);
FileTrajectory trajs = new FileTrajectory();
trajs.frames = new List <Frame>();
foreach (List <string> framelines in frameliness)
{
Frame frame = Frame.FromLines(framelines.ToArray());
trajs.frames.Add(frame);
}
return(trajs);
}
public static Vector[] GetForce(IList <Pdb.Atom> atoms
, IList <Vector> coords = null
, string ff = null // -ff string select Force field, interactive by default. Use -h for information.
// "charmm27", ...
, string water = null // -water enum select Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p
)
{
Vector[] forces;
{
string currdir = HEnvironment.CurrentDirectory;
System.IO.DirectoryInfo temproot = HDirectory.CreateTempDirectory();
HEnvironment.CurrentDirectory = temproot.FullName;
{
if (coords != null)
{
HDebug.Assert(atoms.Count == coords.Count);
}
Pdb.ToFile("conf.pdb", atoms, coords: coords
, headers: new string[] { "CRYST1 " }
);
HFile.WriteAllLines("grompp-nm.mdp"
, new string[] { "; Parameters describing what to do, when to stop and what to save "
, "integrator = md "
, "emtol = 0.001 "
, "emstep = 0.001 ; Energy step size "
, "nsteps = 0 ; Maximum number of (minimization) steps to perform "
, " ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions "
, "nstlist = 1 ; Frequency to update the neighbor list and long range forces "
, "ns_type = grid ; Method to determine neighbor list (simple, grid) "
, "rlist = 1.0 ; Cut-off for making neighbor list (short range forces) ; htna 1.0-1.2 "
, "coulombtype = Shift "
, "rcoulomb = 1.0 "
, "rcoulomb_switch = 0.7 "
, "vdwtype = Shift "
, "rvdw = 1.0 "
, "rvdw_switch = 0.7 "
, " "
, " "
, "nstxout = 1; (100) [steps] frequency to write coordinates to output trajectory file, the last coordinates are always written"
, "nstvout = 1; (100) [steps] frequency to write velocities to output trajectory, the last velocities are always written "
, "nstfout = 1; ( 0) [steps] frequency to write forces to output trajectory. " });
RunPdb2gmx(f: "conf.pdb"
, o: "confout.pdb"
, p: "topol.top"
, i: "posre.itp"
, n: "clean.ndx"
, q: "clean.pdb"
, ff: "charmm27"
, water: "none"
, merge: "all"
, lineStderr: null
, lineStdout: null
);
RunGrompp(f: "grompp-nm.mdp"
, p: "topol.top"
, o: "topol-nm.tpr"
, c: "confout.pdb"
, lineStderr: null
, lineStdout: null
);
RunMdrun(s: "topol-nm.tpr"
, c: "confout.pdb"
, o: "traj.trr"
, g: "md.log"
//, mtx:"hessian.mtx"
//, pf:"pullf.xvg"
//, px:"pullx.xvg"
//, nt:"3"
, lineStderr: null
, lineStdout: null
);
RunGmxdump("traj.txt"
, f: "traj.trr");
FileTrajectory traj = FileTrajectory.FromFile("traj.txt");
forces = traj.frames[0].f;
}
HEnvironment.CurrentDirectory = currdir;
Thread.Sleep(100);
try{ temproot.Delete(true); } catch (Exception) {}
}
HDebug.Assert(forces.Length == atoms.Count);
return(forces);
}
