AMBER Archive (2001)

Subject: Why does water leak!?

From: Sanjeev B.S. (sanjeev_at_mbu.iisc.ernet.in)
Date: Thu May 03 2001 - 04:07:51 CDT

Hello,
        I am new to AMBER6, and I am tring to rerun the simulation that I
did using AMBER5. Checking over hundred control data I started the MD with
what looked to me equivalent values (glancing over the newer options and
neglecting the options that are removed). After 80ps the protein seems
fine, but water has spread! The density is 0.99, box sizes almost the same
but a PDB through a viewer showed lots of waters outside. Suspecting that
periodic boundary conditions might put these waters back into box, I have
tried that using rdparm but did not succeed as it kept on giving problems
and still struggling with it. The input file that I gave is given below,
which I used to rerun after 1ps of MD (which I did to get rid of num_ks
problem on multiprocessors).
        I would be grateful for anyone who helps and/or the
such experiences if one has faced.

Thanks in advance,
-Sanjeev
-------------------------mdin-----------------------------------
First phase of equlibriation (1-4ps)
 &cntrl
    imin=0, irest=1, ntx=7,
    ntt=1, tempi=100., temp0=100.0 tautp=0.1,
    ntp=1, taup=0.2,
    ntb=2, ntc=1, ntf=1,
    nstlim=3000,
    cut=12.0,
    ntcm=1, nsnb=10, nscm=10,
    ntwe=1000,ntwx=1000, ntpr=100
 /
----------------------------------------------------------------
PS:
1) Number of atoms ~18000, including ~2200 solute atoms.
2) rdparm gives "ERROR in dispatchToken: Token string "transform" not
found in tokenlist" on AMBER6, and does something to the restart file
which I used to make a PDB so that PDB itself is not generated on AMBER5
version. So I am in the process of writing my own code for it.