Hello everyone,
I was able to check, it was the periodic boundary condition. After
reimaging I found 2603 Wat in a 3 A radius (2528 in Gromacs) and 4784 5A
radius of the protein (4232 in Gromacs).
Thanks for your help!
István Lőrincz
2016-12-28 9:45 GMT+01:00 I Lőrincz <lorizoli.gmail.com>:
> Thanks to everybody for quick answers and the suggestions! Unfortunately
> the server I was running the simulations on (and has the trajectories) went
> down yesterday. I'll get back to you once I have access back.
>
> István Lőrincz
>
> 2016-12-28 3:08 GMT+01:00 David Case <david.case.rutgers.edu>:
>
>> On Tue, Dec 27, 2016, Chris Moth wrote:
>>
>> > Is there any chance this is a long simulation, and the "missing waters"
>> > have wandered into other periodic cells - and you not wrapped them back
>> > into the main cell for analysis?
>> >
>> > Are the dimensions of the simulation cell also changing dramatically
>> > between AMBER and GROMACS?
>>
>> Or, what is pretty much the same thing: what are the densities of the two
>> simulations? But Chris' suggestion seems like the first one to rule in or
>> out.
>>
>> ....dac
>>
>>
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>
>
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Received on Tue Jan 03 2017 - 16:00:05 PST
