[gmx-users] long-stick molecule solvation

Wed Nov 4 13:53:29 CET 2015

Hi Justin,

thanks for your reply. I actually just followed your tutorial on lysozyme.
I did not set any termini or merge any chains.

Thanks,

Yao

At 2015-11-04 20:44:51, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>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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>>>>>>> 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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> 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
>>>
>>> ==================================================
>>> --
>>> 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
>
>==================================================
>-- 
>Gromacs Users mailing list
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