Hi Yao Yao,
> 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.
You say that you 'guess'. Have you tried visualizing the trajectory to see
what is happening? You could try running some short runs with ntwx set
small, say 10 or so and then visualize it and see what happens.
> ================= 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
> ==============================
These are very short heating phases, just 12.5ps. You also need to
equilibrate the pressure and remove the restraints from the region that will
be QM and allow that to equilibrate BEFORE running QMMM.
Try the following:
MM only NVT weak restraints, tempi=0.0,temp0=300.0,nstlim=100000
MM only NPT no restraints, temp0=300.0,ntb=2,ntp=2,taup=5.0,nstlim=500000
Then try plotting the density, pressure etc for this run and check
everything is stable. Then try switching to QMMM. I suspect the problem is
with your underlying system not being stable than it is with the QMMM
approach.
> =========== 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
> /=================================
Note, your runs are VERY short here. just 100ps is unlikely to be enough to
equilibrate the density. So your system may not be blowing up, the pressure
may just be negative since the box still needs to shrink. If your density is
slowly increasing towards 1 then it just says you are not equilibrated yet.
Run this out for a nanosecond or so and see what the plots look like then.
> 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?
You will need to debug this. The process_mdout file should just be
extracting the values after Density in mdout. It is possible it is not
working for QMMM. You will have to find which values it is extracting to
work out what is going on.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
---------------------------------------------------------
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Oct 15 2011 - 09:30:02 PDT
