[gmx-users] Error when performing MD with heavy atoms frozen

[Kai Hu]

That is good to know, thanks! Can you also tell me if it is possible and
how to include FE atom in the system? Sorry for those many questions.


--Kai

On Fri, Jun 16, 2017 at 1:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/16/17 9:34 AM, Kai Hu wrote:
>
>> Thanks for the fast reply! My system is little bit complicated, it cotains
>> a protein, an organic ligand plus an iron and several water with 100%
>> occupancy. I need to simulate this model system to see how these water
>> interact with ligand and iron. I went through the tutorial Protein with
>> Ligand, succussfully simulate system with ligand.
>> Can u tell me how to model in iron and these water? I would like iron and
>> water oxygens to be frozen at their original positions.
>>
>
> Why not allow for flexibility?  Why freeze the waters?  Not much is likely
> to happen if you do this.  Assuming a frozen configuration is highly
> artificial. Intuitively, you'll get a better representation of water
> dynamics and any induced structural changes with unbiased MD.  What you
> want to do can be done with freezegrps and energygrp_excl if you really
> think it necessary (again, refer to the manual).
>
> -Justin
>
>
> Looking forward to your reply!
>>
>> -Kai
>>
>>
>> On Fri, Jun 16, 2017 at 7:19 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 6/15/17 11:57 AM, Kai Hu wrote:
>>>
>>>> Hi there,
>>>> I am new to GROMACS, went through Lysozeme in Water tutorial and
>>>>
>>> everything
>>>
>>>> runs smoothly.
>>>> I then tried to immobilize all heavy atoms (except H) in md.mdp file by
>>>> specifying freezegrps               = Protein-H       ; Freeze all heavy
>>>> atoms
>>>> freezedim                = Y Y Y             ; Freeze all dimensions
>>>> towards the end of the file. I previous generated a index.ndx file using
>>>> gmx make_ndx command.
>>>>
>>>> This time, a fatal error would show up, saying:
>>>> Fatal error:
>>>> Bond length not finite.
>>>>
>>>> Can anyone tell me briefly what might be wrong that leads to such error?
>>>> Note, if I remove these two commands in md.mdp file, no error would pop
>>>>
>>> up,
>>>
>>>> it seems something must wrong with the freeze commands.
>>>>
>>>>
>>> Freezing is an extremely artificial perturbation and if you're applying a
>>> barostat, you'll get spurious contributions to the virial, as noted in
>>> the
>>> manual.  Application of freezing usually requires corresponding
>>> energygrp_excl.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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> Gromacs Users mailing list
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-- 
Kai Hu

Ph.D. candidate,
Allen's lab, W240-MSC
the Pennsylvania State University
+1-814-777-8651


*"When God closes a door, he always opens a window."*