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
