[gmx-users] npt simulation error
jalemkul at vt.edu
Wed Aug 16 17:52:41 CEST 2017
On 8/15/17 9:22 PM, Mohammad Zahidul Hossain Khan wrote:
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon-r = 4
epsilon-r is used to change the relative dielectric constant; you
shouldn't do this because it will fundamentally break the electrostatic
convention used by all of the "usual" GROMACS force fields.
If you're trying to alter reaction field properties, the keyword is
epsilon-rf. See the manual.
> On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote:
>>> Dear Sir
>>> I am trying to simulate protein_ligand complex using epsilon = 4 and it is
>>> giving the below error
>> What is epsilon = 4?
>> *2 particles communicated to PME rank 4 are more than 2/3 times the cut-off
>>> out of the domain decomposition cell of their charge group in dimension x*
>>> I have no idea how to solve this problem
>> Have you Googled it, or gone to the GROMACS error page, where lots of
>> advice lives? ;)
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
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>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>> jalemkul at vt.edu | (540) 231-3129
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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