Hi,
I followed closely what you recommended, esp. turn on qmmm only in md production run step,
this time still pressure, density and volume are not the expected values, esp. pressure is not 1 bar, but -371 on average. So I guess the system is blowing up.
Here I post my Energy minimization input files, em1.in em2.in, and my equilibration and production run input files, md1.in and md2.in, respectively.
============ em1.in ================
Initial min of our structure QMMM
&cntrl
imin=1, maxcyc=1000, ncyc=500,
cut=8.0, ntb=1
/
Hold the protein fixed
500.0
RES 1
END
END
====================================
============ em2.in ==================
Secondary min of our structure QMMM
&cntrl
imin=1, maxcyc=2500, ncyc=1000,
cut=8.0, ntb=1, ntr=0
/
========================
================= md1.in ============
300K constant temp QMMMMD
&cntrl
imin=0,
ntb=1,
irest=0,
ntx=1,
cut=8.0,
ntr=1,
ntf=2,
ntc=2,
tempi=0.0,
temp0=300.0,
ntt=3,
gamma_ln=1.0,
ntp=0, taup=2.0,pres0=1,
nstlim=12500, dt=0.001,
ntpr=100, ntwx=500, ntwr=1000
/
Keep prtein fixed with weak restraints
10.0
RES 1
END
END
==============================
=========== md2.in ============
300K constant temp QMMMMD
&cntrl
imin=0, ntb=2,irest=1,ntx=5,
cut=8.0, ntc=2, ntf=2,
tempi=300.0, temp0=300.0,
ntt=3, gamma_ln=1,
ntp=1, taup=2.0,pres0=1,
nstlim=50000, dt=0.001,
ntpr=100, ntwx=500, ntwr=1000, ifqnt=1
/
&qmmm
qmmask=':1',
qmcharge=0,
qmtheory=1,
qmshake=1,
qm_ewald=1, qm_pme=1
/=================================
I used process_mdout.perl to process the output, but I am confused when I see the values in summary.DENSITY are quite different from those named "Density" in my .out file.
Has anyone met this before?
Thanks,
Yao
________________________________
From: David A. Case <case.biomaps.rutgers.edu>
To: Yao Yao <yao0o.ymail.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, October 14, 2011 1:22 PM
Subject: Re: [AMBER] QMMMMD blowup
On Fri, Oct 14, 2011, Yao Yao wrote:
> 300K constant temp QMMMMD
> &cntrl
> imin=0, ntb=2,
> cut=8.0, ntc=2, ntf=2,
> tempi=300.0, temp0=300.0,
> ntt=3, gamma_ln=1,
> ntp=1, taup=2.0,pres0=1,
> nstlim=5000, dt=0.002,
> ntpr=10, ntwx=10,ifqnt=1
> /
> &qmmm
> qmmask=':1',
> qmcharge=0,
> qmtheory=1,
> qmshake=1,
> qm_ewald=1, qm_pme=1
> /
Since you don't set irest, it looks like this is the initial equilibration run.
Generally, you should turn on QM/MM only after an initial equilibration with
MM only. Also, we recommed that you first equilibrate with ntb=1,ntp=0, then
move on to ntb=2,ntp=1. Once you have a system that you know is stable with
MM, then you can try a QM/MM run.
You may need much more than 5000 steps to equilibrate, and using the default
value of dt=0.001 during intial equilibration can also help.
...hope this helps....dac
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Received on Fri Oct 14 2011 - 21:00:04 PDT
