[gmx-users] energy_terms

[Mark Abraham]

On 18/12/2011 11:28 AM, Mark Abraham wrote:
> On 18/12/2011 3:56 AM, balaji nagarajan wrote:
>>
>> Dear Users !
>>
>> I can print the values of the bonded and non bonded energy terms of 
>> the protein and the water ,
>>
>> I have used the group option ,
>>
>> I want to know the bonded contribution only from the protein ,
>> in case of the torsion energy term it is only for the protein ,
>>
>> The bond distance and the bond angle , the contribution from the 
>> water is also there , so how one can get these
>> terms for protein alone .
>
> You can't do this during the original simulation, but you can take a 
> completed simulation and use tpbconv on the .tpr and trjconv on the 
> trajectory file to extract the same subset of atoms from each. Now 
> mdrun -rerun on those two partial files can give you the bonded 
> energies of whatever interests you. Whether that bond energy means 
> anything is another matter.

Of course, if you used a rigid water molecule for the simulation, then 
there are already no bonded contributions from water.

Mark

>
> Mark
>
>>
>> thanks in advance
>>
>> ------------------------------------------------------------------------
>>
>>
>> Date: Sat, 17 Dec 2011 17:39:47 +1100
>> From: Mark.Abraham at anu.edu.au
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] energy_terms
>>
>> On 17/12/2011 5:25 PM, balaji nagarajan wrote:
>>
>>     Dear Users !
>>
>>     I have used the energy group option to split the energy terms ,
>>     for the protein and the water.
>>
>>
>> You have split the *non-bonded* terms.
>>
>>
>>     It gives all the terms ,
>>
>>     protein-protein , water-water , water-protein .
>>
>>     I have a doubt ,
>>     the distance and the angle are taken for both water and the
>>     protein ,
>>
>>
>> I don't see what distance and angle you mean.
>>
>>
>>     how one can get these energy terms for protein alone.
>>
>>
>> What energy terms do you want? You have the intra-protein non-bonded 
>> energies above.
>>
>> Mark
>>
>> -- gmx-users mailing list gmx-users at gromacs.org 
>> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the 
>> archive at http://www.gromacs.org/Support/Mailing_Lists/Search before 
>> posting! Please don't post (un)subscribe requests to the list. Use 
>> the www interface or send it to gmx-users-request at gromacs.org. Can't 
>> post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111218/94d318a3/attachment.html>