AMBER Archive (2008)

Subject: RE: AMBER: AMBER minimization problems

From: Ross Walker (
Date: Thu Dec 18 2008 - 11:46:45 CST

Hi Lili,


So I tried this out on my machine and have a number of comments. Firstly
this is a HUGE system, 673,130 atoms. Running on 2 processors of my desktop
this requires 2.6GB of memory, so unless the machine you are running this on
has around 4GB of memory the code will be swapping like crazy which means it
likely isn't hung it is just taking a very long time. If you wait 10 years
or so it may actually finish. The main point is that for a simulation this
large you will need much more than just a dual processor machine to run it.
Firstly a advise you to use PMEMD in place of sander.MPI, this will run much
faster and require a lot less memory (as you increase the number of


You might also want to try setting ntpr=1 - this way you will be able to see
that the minimization hasn't stopped at 500 steps but is in fact just
running very slowly.


Also a few comments on your input file:


water minimization


  imin=1, ntmin=1, nmropt=0,

  maxcyc=2000, ncyc=500, drms=0.1

  ntx=1, irest=0,

  ntpr=500, ntwr=500, iwrap=1,

  ntf=1, ntb=1, cut=8.0, nsnb=10,


  ibelly=0, ntr=1,

  restraint_wt=300.0, restraintmask=':PEG'



nsnb=10, this has no effect on its own, sander and pmemd will build the list
automatically as needed.


restraint_wt=300.0 - this is very large. It is probably okay for the
minimization but not for when you do MD.


You will also have to use the 'old' style of specifying restraints when you
use pmemd.


Good luck,



From: [] On Behalf Of
Lili Peng
Sent: Wednesday, December 17, 2008 8:36 AM
Subject: Re: AMBER: AMBER minimization problems


Hi Ross,

It just stops after the 2nd nstep and the minimization doesn't proceed any
further. I'm attaching my minimization output for your reference.

My input script was:
/sander -O -i -o peg5k_wat_min_vac.out -p -c
peg5k_wat.crd -r peg5k_wat_min_vac.rst -ref peg5k_wat.crd

My .crd and .top files are too large to attach to this email, so I've
uploaded them to my web server here:

Thanks for your help,

2008/12/17 Ross Walker <>

Hi Lili,


What do you mean by 'ends'? Do you get any further output? Any error
messages of any kind? It would also be helpful to see your input file.


All the best



From: [] On Behalf Of
Lili Peng
Sent: Tuesday, December 16, 2008 11:14 PM
Subject: AMBER: AMBER minimization problems



I'm having trouble minimizing a 5000 Dalton polyethylene glycol molecule
solvated in a TIP3PBOX 15 water molecules. The output file I get ends after
the 2nd nstep of 500 (shown below). This is after I've vacuumed minimized
my molecule (and then solvated it in water). I've attached my water
minimization file input file. Do anyone know what the problem could be?



   4.  RESULTS

--------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION using 5000.0 points per unit in tabled values TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 64267381 | TOTAL SIZE OF NONBOND LIST = 130524253

NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.0703E+06 1.2881E+01 4.6850E+01 O 255159

BOND = 16.4676 ANGLE = 8.8005 DIHED = 158.2966 VDWAALS = 255110.9185 EEL = -2325481.7410 HBOND = 0.0000 1-4 VDW = 105.8433 1-4 EEL = -249.6019 RESTRAINT = 0.0000

NSTEP ENERGY RMS GMAX NAME NUMBER 500 -2.6528E+06 9.0587E-01 4.5299E+00 H1 309256

BOND = 182580.9181 ANGLE = 4.6033 DIHED = 157.3146 VDWAALS = 382897.9872 EEL = -3218340.8995 HBOND = 0.0000 1-4 VDW = 103.2430 1-4 EEL = -249.2364 RESTRAINT = 3.5502 EAMBER = -2652846.0697

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