Re: [AMBER] limit exceeded and high temperature

From: Ruth Helena Tichauer <rhtichau.laas.fr>
Date: Fri, 11 Sep 2015 17:40:13 +0200

Hi Jason,

Thank you for the advice, I’ll try it out and will check the minimisation for starters.

I’m already printing every single step and the only error message that I get is: “vlimit exceeded at step..”

Here is the input file (for more details):
                                                   
 &cntrl
  imin=0,
  ntb=0,
  igb=1,
  cut=12.0,
  tempi=0.0, temp0=100.0,
  ntc=2, ntf=2,
  ntt=3, gamma_ln=2.0,
  nstlim=1000, dt=0.0005,
  ntpr=1, ntwx=1,ifqnt=1,
  ntr=1,
  restraintmask = ':170,185,@CA,C,N',
  restraint_wt = 5.0
 /
 &qmmm
  qmmask=':35,59,61,168,169,186-188',
  qmcharge=-2,
  qm_theory='PM3',
  qmshake=0,
  qmcut=12.0,
 /

Forgot to tell that, as you may see, backbone carbons and nitrogens of two residues are constrained.

Thanks a lot,

Ruth
         
> On 11 Sep 2015, at 17:26, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Fri, Sep 11, 2015 at 10:52 AM, Ruth Helena Tichauer <rhtichau.laas.fr <mailto:rhtichau.laas.fr>>
> wrote:
>
>> Hi Amber community,
>>
>> I’m running a molecular dynamics simulation of a protein with its ligand
>> and an Mg +2 ion in implicit solvent although there are tree water
>> molecules in the active region as they are necessary for the reaction to
>> proceed.
>>
>> I’m modeling quantum mechanically (QMMM) a few residues with the PME
>> method, as well as the Mg ion, the tree water molecules and the ligand
>> (which contains phosphates).
>>
>> The structure has been successfully quantum minimised prior to the MD/QMMM
>> run and in the later (which, for now, nstlim=1000 only) the initial
>> temperature is 0°K and the final one is 100°K (tempi=0.0, temp0=100.0)
>>
>> I started with dt=0.002 and no shake options. I got an error message which
>> said: “vlimit exceeded for step..”
>> and also: "This is usually a a symptom of some deeper problem with the
>> energetics of the system”
>>
>
> ​A timestep of 2 fs is about the upper limit of what you can achieve using
> SHAKE and *no* QM and still have stable integration. It is much too large
> with SHAKE and QM.
> ​
>
>
>>
>> Searching on the amber archives, I found that I should decrease dt and add
>> some shake options (ntc=2 and nff=2) in the input file. Yet, these changes
>> (dt=0.001 and even dt=0.0005) didn’t help. Well, by diminishing dt without
>> adding the shake options, the simulation reaches the final step but the
>> temperature and the total energy are incredibly (unrealistically) high.
>>
>
> ​This is caused by very high forces, most likely. Perhaps the structure
> was not minimized well enough (the minimization output prints out the max
> gradient -- you should check that this is decreasing steadily during the
> minimization and reaches a reasonably small value at the end).
>
> Also, try a simulation where you print out every step and see if the
> trajectory or output file gives any clues as to what is going wrong.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Sep 11 2015 - 09:00:03 PDT
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