[gmx-users] Inconsistent Shifts

[Justin Lemkul]

On 2/25/18 6:27 PM, Dallas Warren wrote:
> Iman,
>
> As I mentioned earlier, does the warning actually stop the simulation
> from running/completing?  If not, then simply ignore it.
>
> One of the developers will need to chime in here about the error itself.

It would be helpful to know what exactly was being done beyond "using 
some commands in gromacs" to help here.

If it was an analysis tool, then there's no significance to this 
message, given the fact that there are periodic molecules. If it was 
from trjconv, again, we would have to know the *exact* command being used.

-Justin

> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
>
>
> On 25 February 2018 at 20:34, Iman Ahmadabadi
> <imanahmadabadi75 at gmail.com> wrote:
>> Dear Dallas,
>>
>> I have tried the 2016.5 version of gromacs that it has the same warning
>> about the inconsistent shifts. I don't know why it should arises as a
>> warning and what is the problem. Is there another way to fix this warning?
>>
>> Sincerely
>> Iman
>>
>> On Wed, Feb 21, 2018 at 11:26 AM, Iman Ahmadabadi <
>> imanahmadabadi75 at gmail.com> wrote:
>>
>>> Dear Dallas,
>>>
>>> Yes, the system has periodic molecules (periodic-molecules = yes) and the
>>> version of gromacs is 5.1.2. So, I should use for calculating the
>>> properties of the system by gromacs 2016 and newer ones?
>>>
>>> Respectfully,
>>> Iman
>>>
>>> On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi <
>>> imanahmadabadi75 at gmail.com> wrote:
>>>
>>>> Dear Gromacs users,
>>>>
>>>> In using some commands in gromacs, the sentence "There were 240
>>>> inconsistent shifts. Check your topology" come up on the screen and I don't
>>>> know what is wrong in my topology file, however it calculates correctly the
>>>> features of the system but I would like to know the reason of this warning.
>>>>
>>>> Respectfully,
>>>> Iman
>>>>
>>>
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-- 
==================================================

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

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