From: Amesh Patel <paxabp_at_nottingham.ac.uk>
Date: Fri 02 Nov 2001 05:09:57 +0000

i am having a problem restarting equilibration. i have two protein systems in implicit solvent (idiel=0). one is ~1600 atoms and the other is 3200 atoms in size. i have equilibrated both systems after minimization such that the temperature and total energy after 800ps were stable (very much stable) - gradual warming from 0-298K over 50ps. when i do further molecular dynamics with the 3200atom system, it carries on as before, but when i subject the 1600 atom system to EXACTLY the same input file as the 3200atom follow-on MD input file, the energy and temperature of the 1600 atom protein looks to be too large and AMBER cannot cope with it. i have checked the structure of the 1600 atom protein after equilibration and it is still intact and looks reasonable. here is the md.in i am using to follow on MD after equilibration:

   irest=1, ntx=5,
   ntpr=50, idiel=0,
   cut=10, nsnb=99999, scee=1.2,
   nrun=1, nstlim=10000, init=4, dt=0.001,
   ntwe=500, ntwx=500,
   temp0=298, ntt=5,
   ibelly=1, nmropt=1,
   type= 'END',

ATOM 1 3290
ATOM 3292 3301

if anyone is out there who has some sort of clue about it all, please help!!! thanking you in advancd.
a. patel.
Received on Thu Nov 01 2001 - 21:09:57 PST
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