On Mar 14, 2013, at 2:23 PM, R. Xiong wrote:
> You are right. My QM region does have multiple unbonded molecules. I
> thought there is some trick in Amber that can avoid the problem. Ok, thanks
> for your suggestion.
>
If your problem is something like water diffusing away, you can set up
a one-sided flat well potential with a mild force constant to keep things
in a sphere centered on some atom or point like the center of mass of
the QM region.
>
>
> On Thu, Mar 14, 2013 at 2:54 PM, Matthew Zwier <mczwier.gmail.com> wrote:
>
>> Does your QM region span multiple (unbonded) molecules? If so, iwrap=1 can
>> cause one molecule to wrap around the box while leaving the other in place,
>> which can lead to a QM crash. (The MM routines consider nearest neighbors,
>> but I've seen the QM routines not do so, or at least terminate a simulation
>> before it even tries). We tend to recenter our restart files around one of
>> the QM molecules to avoid this problem.
>>
>> Cheers,
>> Matt Zwier
>>
>>
>> On Thu, Mar 14, 2013 at 2:14 PM, R. Xiong <rchxiong.gmail.com> wrote:
>>
>>> Yes, that was the message. So I just got lucky by using iwrap=0? No way
>> to
>>> solve this problem? Thanks.
>>>
>>>
>>> On Thu, Mar 14, 2013 at 1:29 PM, Gustavo Seabra <
>> gustavo.seabra.gmail.com
>>>> wrote:
>>>
>>>> If I had to guess, I'd guess that you have a QM region such that
>>>>
>>>> (QM size + cutoff) > (0.5 * box side),
>>>>
>>>> such that in periodic boundary calculations the QM region can see its
>>>> image, which is not allowed in Amber. However, this should be
>> independent
>>>> of iwrap: it would appear anytime you try o use periodic boundary
>>>> conditions.
>>>>
>>>> Could you reproduce the actual message here? That would make the
>> guessing
>>>> lot easier.
>>>>
>>>>
>>>> Gustavo Seabra
>>>> Professor Adjunto
>>>> Departamento de Química Fundamental
>>>> Universidade Federal de Pernambuco
>>>> Fone: +55-81-2126-7450
>>>>
>>>>
>>>> On Thu, Mar 14, 2013 at 11:42 AM, R. Xiong <rchxiong.gmail.com> wrote:
>>>>
>>>>> I am running QM/MM simulations using Amber with iwrap=1. It was
>> running
>>>>> successfully, but when I restart the program, the program crashes
>>> because
>>>>> of QM/MM region is too large. I believe this should be caused by
>> iwrap
>>>>> option. If iwrap=0, this problem will disappear, but my question is
>>> that
>>>> if
>>>>> there is any way to deal with the problem when still using iwrap=1.
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--
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Received on Thu Mar 14 2013 - 13:00:04 PDT
