[gmx-users] eneconv with -dt flag

[Mark Abraham]

On 8/06/2012 11:51 PM, Turgay Cakmak wrote:
> Thanks Mark.
> I want to calculate Coulomb and Lennard-Jones energies using 
> total_dt100.edr .
> But, I am not sure I can get the correct energies?

Neither am I. Only you know the history of these .edr files.

Mark

>
> Turgay
>
> 2012/6/8 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
>
>     On 8/06/2012 10:40 PM, Turgay Cakmak wrote:
>>
>>     Hi all,
>>
>>     I have encountered a problem using eneconv with -dt flag.
>>     I have several energy files. Firstly, I concatenated them using
>>     the following.
>>
>>     eneconv-f first.edr   second.edr  ....  -settime -o total.edr
>>
>>     But, total.edr is so large. To reduce the size of file, I used
>>     the below command:
>>
>>     eneconv -f  total.edr  -dt  100 -o  total_dt100.edr
>>
>>     But, I get the following warning:
>>     *.*
>>     *.*
>>
>>     WARNING: missing energy sums at time 69984.000000
>>
>>     WARNING: missing energy sums at time 69988.000000
>>
>>     WARNING: missing energy sums at time 69992.000000
>>
>>     WARNING: missing energy sums at time 69996.000000
>>     Reading energy frame  35000 time 70000.000
>>     WARNING: missing energy sums at time 70000.000000
>>     Last energy frame read 35000 time 70000.000
>>     Last step written from energy.edr: t 70000, step 35000000
>>
>>     Last frame written was at step at step 35000000, time 70000.000000
>>     Wrote 701 frames
>
>     At some point something did something to break the usual format of
>     the files... but we can have no idea what.
>
>
>>
>>     Eventually, I get the "total_dt100.edr". But, I am not sure I
>>     could continue using this file.
>>     If someone could help me, I would be glad.
>
>     Depends what you want to use it for.
>
>
>     Mark
>
>     --
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