[gmx-users] long-stick molecule solvation

[Justin Lemkul]

On 11/4/15 7:34 AM, xy21hb wrote:
> Dear Justin,
>
> Just in case you are interested, the protein is 4KE2.
>

That doesn't really help much.  My hunch is something is wrong with your 
topology, so likely you set termini incorrectly, merged chains inappropriately, 
etc.  That's the only way bonded interactions would be at such long distances. 
If you can provide an exact listing of your commands, pdb2gmx output, and the 
snippet of the .log I requested, that would be helpful.

-Justin

> Thanks,
>
> Yao
>
>
>
>
>
>
>
>
>
> At 2015-11-04 20:18:23, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>
>>
>> On 11/4/15 5:11 AM, xy21hb wrote:
>>> Dear Justin,
>>>
>>> Attached is the em.log file. Could you get a chance to take a look at it?
>>>
>>
>> I see nothing obvious, but the use of -rdd 4 is perhaps precluding important
>> information.  Please provide the text from the .log file without this option
>> (just run with default DD settings).  It may be more informative.
>>
>> -Justin
>>
>>> Thanks,
>>>
>>> Yao
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> At 2015-11-04 07:35:46, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>> On 11/3/15 6:33 PM, xy21hb wrote:
>>>>> Dear all,
>>>>>
>>>>> Thanks for the reply. However, my system is just a long finite protein with its length of 220 A.
>>>>> Any further suggestion would be appreciated.
>>>>>
>>>>
>>>> The DD information from the .log file would be informative.  No sensible protein
>>>> system should ever lead to a minimum DD cell size like that.  Something is
>>>> either wrong in your topology or wrong in your .mdp settings, but without the
>>>> information from the .log file, we're working blind.
>>>>
>>>> -Justin
>>>>
>>>>> Best,
>>>>>
>>>>> Yao
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> At 2015-11-04 06:13:11, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>>>>>
>>>>>>
>>>>>> On 11/3/15 9:57 AM, xy21hb wrote:
>>>>>>> Dear all,
>>>>>>>
>>>>>>> I have a long-stick "carbon-nanotube" like protein to solvate with its length of ~ 220 A and diameter of 50 A.
>>>>>>
>>>>>> Does this imply that you have connectivity across PBC, like an "infinite" nanotube?
>>>>>>
>>>>>>> I tried using a triclinic box with the longest box axis aligned to the C-alpha of the protein, and the protein seems to be properly solvated.
>>>>>>> However, energy minimization with GROMACS 5.0 shows,
>>>>>>> "There is no domain decomposition for 48 ranks that is compatible with the given box and a minimum cell size of 9.59877 nm"
>>>>>>> Any suggestions on that?
>>>>>>>
>>>>>>
>>>>>> If the answer to the above question is "yes," then you need "periodic_molecules
>>>>>> = yes" in your .mdp file.
>>>>>>
>>>>>> -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
>>
>> ==================================================
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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

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