AMBER Archive (2001)

Subject: equilibration

From: Amesh Patel (paxabp_at_nottingham.ac.uk)
Date: Thu Nov 01 2001 - 23:09:57 CST

hello!
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:

 &cntrl
   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,
 &end
 &wt
   type= 'END',
 &end
 DISANG=restraints.f

belly
ATOM 1 3290
ATOM 3292 3301
END
END

if anyone is out there who has some sort of clue about it all, please help!!! thanking you in advancd.
a. patel.