Hello Fabricio and Feng,
Thanks very much for your replies.
Yeah, the simulation was not finished as I did not see the output of the
biased potential, then
I canceled the simulation. I will then try to finish the simulation and
do the analysis.
All the best,
Qinghua
On 07/15/2017 05:56 AM, Feng Pan wrote:
> Hi, Qinghua
>
> Fabricio is right. It seems your simulation is interrupted during the
> simulation and not finish.
> So the bias files will not be written.
>
> Besides, I found another possible problem of the example run is that
> because the water box here
> is small, the run of explicit solvent may have a problem in PMEMD. Because
> box size should be larger
> than 2*(cut+skinnb)
> I suggest you change cut=8.0 and add
> &ewald
> skinnb = 1
> &end
> to the mdin files. And everything will be good.
>
> Feng
>
> On Thu, Jul 13, 2017 at 5:45 PM, Qinghua Liao <scorpio.liao.gmail.com>
> wrote:
>
>> Hello Feng,
>>
>> Thanks very much for your reply! The input and output files are in the
>> Dropbox:
>>
>> https://www.dropbox.com/s/1b9gl9te86xvjci/dialanine-2d.zip?dl=0
>>
>>
>> All the best,
>> Qinghua
>>
>>
>> On 07/13/2017 11:24 PM, Feng Pan wrote:
>>
>>> Hi, Qinghua
>>>
>>> The suffix should not matter, can you send me your mdin and mdout files
>>> to check?
>>>
>>> Feng
>>>
>>> On Wed, Jul 12, 2017 at 8:37 AM, Qinghua Liao <scorpio.liao.gmail.com>
>>> wrote:
>>>
>>> Hello All,
>>>> I tried to run adaptively biased MD simulations with multiple walkers on
>>>> the dialanine system from the tutorial with Amber 16:
>>>> http://ambermd.org/tutorials/advanced/tutorial31/
>>>>
>>>> I did not change anything of the input files, the simulation ran well, I
>>>> can get the output for monitor_file. But I found one problem that I did
>>>> not get the output files of umbrella_file and wt_umbrella_file: bias.nc
>>>> and wt_bias.nc.
>>>>
>>>> And I found that the files for umbrella_file and wt_umbrella_file in the
>>>> test examples are all empty. Could someone give some tips here?
>>>>
>>>> One more question, is suffix of nc necessary for the files, or any
>>>> suffix should be OK? Thanks a lot!
>>>>
>>>>
>>>> All the best,
>>>> Qinghua
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>
>
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Received on Sat Jul 15 2017 - 02:30:02 PDT
