[AMBER] 3D-RISM in NAB AmberTools: what is tolerance and initial guess

From: Andrey Frolov <frolov.mis.mpg.de>
Date: Thu, 01 Jul 2010 18:09:51 +0200

Dear NAB and 3D-RISM Developers,

I would like to run some simulation with 3D-RISM, and after reading the
Manual for the AmberTools and playing with the program, several
questions appeared:

How to run one point calculation of 3D-RISM in NAB so that to have the
solvent distribution functions saved on the disk?
I have to run 1 step of MD simulation with 0 K temperature and zero
velocities on atoms to get 3D-distributions - so actually i calculate
the same conformation twice. The only way to save 3D functions, that is
written in AmberTools manual, is to use ntwrism key:
But i have to run at least one step of MD or energy minimization (2
energy evaluations) to save functions.

Does the 3D-RISM take the solution of the previous iteration as an
initial guess for next iteration of MD or energy maximization?
If so, why when i run MD where the coordinates of a molecule do not
change at all, the initial error (tolerance) of 3D RISM is about 10-3 in
my case, but the previous iteration converged to 10-11?
See the NAB input at the end of the message.

I would be very pleased if you know something about the questions and
drop me a message.

Thank you very much.
Andrey Frolov, PhD student at Max Planck Institute for Mathematics in
the Sciences, Germany

PS: NAB input:
// carry out molecular mechanics minimization and some simple dynamics
molecule m, mi;
residue tmp_res;
int ier;
float m_xyz[ dynamic ], f_xyz[ dynamic ], v[ dynamic ];
float dgrad, energy, dummy[2];
string F, F2;
matrix new_tr;

F = "Gly.pdb";
F2 = "Gly.top";
m = getpdb(F);
allocate m_xyz[ 3*m.natoms ]; allocate f_xyz[ 3*m.natoms ];
allocate v[ 3*m.natoms ];
setxyz_from_mol( m, NULL, m_xyz );
mm_options("ntpr=1, cut=999.0"); //No solute-solute CUTOFF
mm_options("rism=1, closure=1, buffer=12"); //Use 3D-RISM-KH
mm_options("grdspcx=0.5, grdspcy=0.5, grdspcz=0.5"); //Use 3D-RISM-KH
mm_options("mdiis_del=0.7, mdiis_vec=5, mdiis_method=1, maxstep=1000,
mm_options("xvvfile=wat.xvv"); //1D-RISM input
mm_options("tolerance=1e-11"); //Low tolerance
mm_options("solvcut=999.0"); //No solute-solvent
mm_options("centering=2"); //Center solute
mm_options("ntwrism=1, guvfile=guv_GLY, huvfile=huv_GLY, cuvfile=cuv_GLY");
// MD simulation
mme_init( m, NULL, "::ZZZ", dummy, NULL );
mm_options("zerov=1, tempi=0.0");
md( 3*m.natoms, 1, m_xyz, f_xyz, v, mme );
printf( "Iteration is complete, energy %8.3f\n", energy );

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Received on Thu Jul 01 2010 - 09:30:03 PDT
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