[gmx-users] Comm-mode

[Amin Rouy]

Dear Justin,

If we do not use comm-mode, which quantity might be changed after
simulations?

Can we remove center of mass after the simulation done?

On Sat, Mar 10, 2018 at 6:36 PM, Amin Rouy <aminrou1986 at gmail.com> wrote:

> thank you so much.
>
> On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>