[gmx-users] saving coordinates

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello Justin,
> 
> THanks for your reply.
> 
> Suppose any atom that leaves a simulation box by, say, the right-hand
> face, then enters the simulation box by the left-hand face.
> 
> For these atom how gromacs save the coordinate.
> Does it save the coordinate when it enter from left-hand face?
> 

Presumably.  Look in the code, but I suspect this is indeed the case and the 
reason why trjconv -pbc nojump and other such operations are useful.

-Justin

> Nilesh
> 
> On Wed, April 13, 2011 9:26 pm, Justin A. Lemkul wrote:
> 
>> Nilesh Dhumal wrote:
>>
>>> Hello,
>>>
>>>
>>>
>>> If some part of molecule is outside the box. How Gromacs save the
>>> coordinates in trajectory.
>>>
>> There is no such thing as "outside" in a periodic system.
>>
>>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condit
>> ions
>>
>> -Justin
>>
>>
>>> Nilesh
>>>
>>>
>>>
>>>
>> --
>> ========================================
>>
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org. Can't post? Read
>> http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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