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

[Justin Lemkul]

On 6/16/17 1:52 PM, Kai Hu wrote:
> 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.
> 

Atoms or ions?  In either case, transition metals are hard to deal with and most 
additive force fields have very crude parameters or are very specific for, e.g. 
heme, not free ions in solution.

-Justin

> 
> --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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> 
> 
> 

-- 
==================================================

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

==================================================