Yes, I used cpptraj and that gave me the warnings.
Victoria
> On 21 Feb 2021, at 13:27, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> how did you convert to crd, with cpptraj? which program gave you those
> warnings?
>
>> On Sun, Feb 21, 2021 at 7:58 AM Victoria E Hill <vehill1.sheffield.ac.uk>
>> wrote:
>>
>> Thank-you for your reply.
>>
>> I ran my simulations as .nc files but had to change them to .crd in order
>> to visualise them with VMD (I’m on a windows computer) and got the ‘atoms
>> overlapping at origin’ warnings which I saw online were due to corruption.
>> Is this not the case?
>>
>> Even so, why are netcdf less prone to corruption?
>>
>> Thanks,
>> Victoria
>>
>>>> On 21 Feb 2021, at 10:57, Maria Nagan <maria.c.nagan.gmail.com> wrote:
>>>
>>> Are you sure they’re corrupted and not just netcdf trajectories?
>> Sometimes with the mdcrd text files I’ve had corruption but not on only 10
>> ns. Also sometimes the transfer process affects this. Make sure you’re
>> using netcdf files. They are less prone to corruption.
>>>
>>>> On Feb 20, 2021, at 11:36 AM, Victoria E Hill <vehill1.sheffield.ac.uk>
>> wrote:
>>>>
>>>> Hi,
>>>>
>>>> I have been running some 10 ns simulations and almost all are
>> corrupted. I
>>>> know how to fix this with 'skipbadframes' but I was wondering why this
>>>> happens? As I wasn't able to find an explanation online.
>>>>
>>>> Thanks,
>>>> Victoria
>>>>
>>>> --
>>>> *Victoria Hill*
>>>>
>>>> PhD student, Craggs lab
>>>> Department of Chemistry
>>>> University of Sheffield
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Received on Sun Feb 21 2021 - 06:00:03 PST
