AMBER Archive (2009)

Subject: RE: [AMBER] temperature rises with igb=1

From: Ross Walker (
Date: Tue Mar 17 2009 - 11:53:04 CDT

Hi Bala,

> **
> &cntrl
> imin=0,ntx=1,irest=0,ntpr=100,ntwr=500,ntwx=500,nstlim=20000,dt=0.001,temp
> i=100.0,temp0=300.0,
> tautp=0.5,
> ntt=3,gamma_ln=1.0,cut=12,ntc=2,ntf=2,tol=0.000001,ntr=1,restraint_wt=25,r
> estraintmask=':1-22',
> ntb=0,igb=1,intdiel=1,extdiel=80,saltcon=0.1,gbsa=1,rgbmax=15
> /

tautp will be ignored when ntt=3. A restraint_wt of 25 is pretty high for
MD. Something like 5 would probably be better. If your initial structure is
strained you might find that a lot of potential energy is quickly dumped
into the springs as kinetic energy which might take a while to equilibrate

You also don't say how many atoms you have here. The less atoms you have the
more noise there will be on the kinetic energy and thus temperature.

Cut=12 is probably way too small for GB and is leading to a net heating of
your system that the thermostat doesn't keep up with. Hence your temperature
is always above the target temperature. Ideally with GB you should not use a
cut off - set cut=999.0, or at the very least make it 18.0 or more. Although
from the *'s in your output below I think you have more immediate problems
than just the cut off.
> *5.out*
> A V E R A G E S O V E R 100000 S T E P S
> NSTEP = 100000 TIME(PS) = 220.000 TEMP(K) = 340.17 PRESS =
> 0.0

> *6.out* A V E R A G E S O V E R 100000 S T E P S
> NSTEP = 100000 TIME(PS) = 320.000 TEMP(K) =********* PRESS =
> 0.0
> Etot = NaN EKtot = 3568123.6676 EPtot = NaN
> BOND = 851450.1246 ANGLE = 15111.5468 DIHED =
> 1984.8352
> 1-4 NB = 1179.4403 1-4 EEL = -2064.5821 VDWAALS =
> 155.2364
> EELEC = 404.5486 EGB = NaN RESTRAINT =
> 639525195.9927
> ESURF= 28.9927
> EAMBER (non-restraint) = NaN

Your system has blown up. This can be from a combination of things although
often occurs because your starting structure was highly strained. The tough
restraints you used were probably sufficient to hold it together but as you
relaxed them the strained system just flew apart. I suggest you very
carefully look at the trajectory files produced and see if you can see what
causes the system to blow up. Note your bond energy in 6.out above is VERY
high. You can also try running with ntwx=1 or 5 or so this will allow you to
watch how things blow up. I suspect the problem started to occur from the
very beginning so you should look carefully there. Also rerun step 6 with
ntwx=1 and watch what happens.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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