[gmx-users] Comm-mode

[Justin Lemkul]

On 3/10/18 12:31 PM, Amin Rouy wrote:
> Thank you Justin.
> What if we do not know the phase of the final result? of if we are in 2
> phase region (gas-liquid)

If you're applying PBC you have to use linear as your comm-mode (grompp 
will fail otherwise, so that's a pretty good hint).

-Justin

> On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 3/10/18 12:17 PM, Amin Rouy wrote:
>>
>>> Dear Gromacs people,
>>>
>>> I have a question please.
>>>
>>> In which condition we must use center of mass removal? Is that optional or
>>> necessary?
>>>
>> Typically necessary.
>>
>> and how to know which mode (linear or angular) is better for our
>>> simulations?
>>>
>> Linear is only for condensed-phase systems, angular is only for vacuum
>> simulations.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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