AMBER Archive (2007)

Subject: RE: AMBER: MD simulation error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jul 25 2007 - 12:54:30 CDT

Hi Lili,
 
You are writing to the trajectory file on every MD step ntwx=1 - really you
only want to do this for debugging over short <1000 steps runs. When you
switch to running nanosecond long MD sims you should set NTWX to something
like 250 or even 500 to 1000 depending on how often you want to save the
coordinates. Note trajectory files can get very very large. You don't say
how big your system is but consider a system of 50,000 atoms. Writing a
formatted trajectory file which is uncompressed needs 8 bytes per coordinate
so 24 bytes per atom per frame. So for 50,000 atoms this is approx 1.1 Meg
per frame. If you run a 100,000 step simulation writing on every step to the
mdcrd file then your mdcrd file will end up 112 GB!
 
Even if you dump only every 1000 steps you will still get a 100MB trajectory
file so make sure you have sufficient disk space available to run on. If you
are running on a cluster you likely have a quota on your home directory so
will need to write to a scratch directory that has more space available.
Check with the admin of the machine to find out where very large files
should be written during a run.
 
All the best
Ross

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| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Lili Peng
Sent: Wednesday, July 25, 2007 10:38
To: amber_at_scripps.edu
Subject: Re: AMBER: MD simulation error

Thank you Drs. Case and Walker for your insightful comments. The only
reason why I have a large timestep is that I initially tried it with
dt=0.001, but I get the error:

"forrt1: Disk quota exceeded.
forrt1: severe (38) error during write, unit 12, file
/users/lpeng/md_classical10000.mdcrd"

I wonder if this has anything to do with Amber (my guess is a no). I'm
accessing AMBER via SDSC's Teragrid machine, and I presume that it's because
of my disk space on the SDSC server. Any thoughts?

Thanks again,
Lili

On 7/24/07, Ross Walker <ross_at_rosswalker.co.uk> wrote:

Hi Lili,
 
Most probably it is to do with time step - you are suing a 5fs time step and
while you fix all bonds (ntf=3, ntc=3) this is still likely too large - take
a look at your trajectory file and see what it looks like. Note I don't
think ntf>2 is used much so you may want to check that it actually works
properly for your system - is there a reason why you want to keep all the
bonds fixed? You should note that most things have not been parameterized to
run in this mode so I would be very cautious of your results - make sure you
can prove that your choice to keep the bonds fixed is justified - I.e.
perhaps try this out on some model systems and show that you can recover the
same results for the entity you are interested in whether you fix all bonds
or just bonds to hydrogen.
 
You also have an extremely large gamma_ln value.
 
All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key
available on request |

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.

 

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Lili Peng
Sent: Tuesday, July 24, 2007 16:54
To: amber_at_scripps.edu
Subject: AMBER: MD simulation error

Dear all,

I am getting the following error for my MD simulation:

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
        
        
        
     NITER, NIT, LL, I and J are : 0 1 7 16 28
        
     Note: This is usually a symptom of some deeper
        
     problem with the energetics of the system.
        

My input file is the following:

310K constant temp MD
 &cntrl
  imin=0, ntb=1,
  cut=8.0, ntc=3, ntf=3,
  tempi=310.0, temp0=310.0,
  ntt=3, gamma_ln=50,
  nstlim=10000, dt= 0.005,
  ntpr=1, ntwx=1,
 /

Does anyone have any idea why this occurs? Does it have anything to do with
the timestep?

Thank you for your time,
Lili

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