[gmx-users] long-stick molecule solvation

[xy21hb]

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.

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
>
>-- 
>==================================================
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>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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