[gmx-users] Electrostatic interaction energy

[Turgay Cakmak]

Hi all,

I have 2 questions related to the electrostatic energy of the system..

1) Is *total electrostatic energy* equal to *Coulomb-(SR)* + *Coul.-recip*.
OR *Coulomb-14* + *Coulomb-(SR)* + *Coul.-recip*. I am so confused.

I specified in my .mdp file;
coulombtype = PME
rvdw = 1.0
rlist = 1.0
rcoulomb = 1.0
fourierspacing = 0.16
pme_order = 4
ewald_rtol = 1e-5

2) I want to calculate electrostatic interaction energy between 2 residues
in my system which has 10 peptides in total. But I think, I should have
specified the energy groups composed of that 2  residues in my mdp file
before starting the simulation. So in this case, is there any way to get
this interaction energy OR can I just calculate the electrostatic energy of
the whole system?

Thanks in advance,

Turgay



2012/6/8 Mark Abraham <Mark.Abraham at anu.edu.au>

>  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>
>
>>  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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>
>
>
>
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