Sirs and Madames:
I am inexperienced in MD calculations and most certainly am making an
elementary mistake. I was attempting to do a pedagogical calculation for
my own welfare and encountered problems. I attempted to simulate a
methanol molecule in a box of water; the water box blows up (V-->
infinity). Here are the details of the protocol I followed:
1.) I minimized until I observed convergence in total energy within
0.005 (x 10^3).
2.) I heated for 20ps using NVT. There were no obvious vacuum bubbles,
but I am inexperienced. I used 1.0 for the Langevin thermostat collision
frequency, purely out of desperation to regulate temperature properly (I
gather 2 is a more efficient choice, normally?). My input file is posted
at the end of this email.
3.) I "equilibrated" (tried to, anyway) using NPT, first for 30ps, then
300ps out of desperation (no difference). I first used 2fs time steps,
then 1fs out of desperation in case of instability (no difference). I
changed the van der Waals cutoff from 8.0 to 10.0, no difference. I
changed the Langevin collision frequency to induce less (1.0 to 2.0)
purely out of desperation to try something. The density of the
simulation increases linearly as a function of time, no matter what.
Befuddled, I got to the point that I just copy/pasted Amber tutorial
files. Same result. Input file at the end of email.
Watching the trajectory of the box in VMD gives me the enjoyable visual
of methanol becoming slowly unsolvated, as the waters enter the void.
Perhaps I am making a mistake in input file prep.
a.) I did an obscenely simplistic Gaussian optimization of methanol,
read that into antechamber (just making a PDB from a coupled cluster
optimization did not work, something was wrong with the file format
conversion to mol2a).
b.) parmchk revealed all the methanol parameters were there, anyway
c.) made a solvatebox with TIP3P waters, 10.0 box.
This utter failure to change things, no matter what, suggests I am
making a very elementary mistake. Thoughts?
*************************************************************************
Heating Input File
Heat
&cntrl
imin=0,
ntx=1,
irest=0,
nstlim=10000,
dt=0.002,
ntf=2,
ntc=2,
tempi=0.0,
temp0=300.0,
ntpr=100,
ntwx=100,
cut=8.0,
ntb=1,
ntp=0,
ntt=3,
gamma_ln=1.0,
nmropt=1,
ig=-1,
/
&wt type='TEMP0', istep1=0, istep2=9000, value1=0.0, value2=300.0 /
&wt type='TEMP0', istep1=9001, istep2=10000, value1=300.0, value2=300. /
&wt type='END' /
*********************************************
Not-so-equilibrated input file
Production
&cntrl
imin=0,
ntx=5,
irest=1,
nstlim=30000,
dt=0.001,
ntf=2,
ntc=2,
temp0=300.0,
ntpr=100,
ntwx=100,
cut=8.0,
ntb=2,
ntp=1,
ntt=3,
gamma_ln=2.0,
ig=-1,
/
--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
Nigel Richards Research Group
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
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Received on Sun Feb 08 2015 - 20:30:03 PST
