AMBER: GB/SA/LD parallel sander

From: Lwin, ThuZar <>
Date: Mon, 6 Jun 2005 11:48:27 -0500

Dear Amber users,
    I am doing simulation on a homo tetramer (2116 atoms) using Generalized Born solvation model (igb=5) with surface area. I use Langevin Dynamics to control the system temperature and amber 8 sander compiled for parallel processors. I run multiple simulations, each for 5 ns. Most of my simulations behaved as expected except for one run, in which the rmsd analysis showed significant deviation from my reference crystal structure. I tried to investigate the cause of the problem and found that if I take away one of the three (igb=5, Langevin Dynamic, Parallel Computing), the problem seems to have gone away. I am wondering what may have gone wrong in this particular simulation.
     When I looked at the structure at the end of this simulation, the helix in each monomer is forming a kink in similar fashion. I wonder if each of the processors uses the same sequence of random numbers, causing the structural change in each of the four monomers to be very similar. Here is my input file for production run.
   imin = 0,
   ntx = 5, irest = 1,
   ntpr = 500, ntwx = 500, ntwr = 50000,
   ntf = 2, ntb = 0, igb = 5, gbsa = 1, rgbmax = 30, saltcon=0.1,
   cut = 30.,
   nstlim = 2500000, dt = 0.002, nscm = 1000, nrespa = 1,
   temp0 = 300, tempi = 300, ntt = 3, gamma_ln=0.5,
   ntc = 2, tol = 0.00001,
 Thank you,

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Received on Mon Jun 06 2005 - 17:53:00 PDT
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