AMBER Archive (2008)

Subject: Re: AMBER: energy leakage?

From: Sally Pias (sallypias_at_gmail.com)
Date: Thu Oct 23 2008 - 09:47:28 CDT

Thank you for the helpful information. Yes, the conformation of the
molecule is changing appreciably during the simulation. I am working
on improving the starting structure, in case that is a factor.

I used the following input parameters:

&cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 1,
  taup = 2.0, # I realize that this parameter is out of place here.
                    # It was left in after copying the input file from
the constant pressure equilibration.
                    # My guess is that it would not affect a constant
volume simulation.
                    # Other simulations with no value specified for
TAUP also showed heating.
  cut = 10, ntr = 0,
  ntc = 2, ntf = 2,
  tempi = 300.0, temp0 = 300.0,
  ntt = 0,
  nstlim = 500000, dt = 0.002, # I will change dt to 0.001, as you
have suggested.
  ntpr = 250, ntwx = 250, ntwr = 10000,
/

I will change TOL and DSUM_TOL to the smaller values you have
recommended. Are there any other input parameters or starting
conditions that are likely to affect heating?

Thank you.

Sally

On Thu, Oct 23, 2008 at 5:00 AM, David A. Case <case_at_biomaps.rutgers.edu> wrote:
> On Thu, Oct 23, 2008, Sally Pias wrote:
>
>> I have been
>> unable to maintain constant temperature (at 300 K) upon switching from
>> ntt=3 to ntt=0. In previous simulations, the temperature increased
>> gradually from 298 K (after an initial dip) to 310 K over 30
>> nanoseconds.
>
> This is excessive heating, but it is hard to know the cause without knowing
> what input parameters you used. Good energy conservation with ntt=0 generally
> requires setting dt=0.001, tol=0.0000005 (or thereabouts), and
> dsum_tol=0.000001. There may be other problems as well that can lead to
> significant heating, especially if the conformation of the system is changing
> during the simulation.
>
> ...good luck...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu