[gmx-users] long-stick molecule solvation

[xy21hb]

Dear Justin,

Attached is the em.log file. Could you get a chance to take a look at it?

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
>
>==================================================
>-- 
>Gromacs Users mailing list
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