[gmx-users] decomposing the energy

[Mark Abraham]

On 15/05/2011 12:01 AM, Sikandar Mashayak wrote:
> Hey Mark
>
> Do you mean removing all bond definitions from topology file, when you 
> say well constructed topology to exclude all bonded-interactions in rerun?

I said you can decompose the bonded interactions. You can have none by 
removing all bonded interactions, but that won't save you any 
significant time, nor serve any other purpose.

Mark

>
> thanks
> sikandar
>
> On Sat, May 14, 2011 at 8:01 AM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 14/05/2011 10:52 PM, XAvier Periole wrote:
>
>
>         Two things you have to be careful about:
>         1- use trr trajectory files. xtc precision is not sufficient
>         and it will give a lot of discrepancies at least for the
>         bonded terms.
>         2- set the nstlist to 1 as the neiboring list should be
>         undated for each frame and not every 5/10 as it is normally
>         set in a regular mdp file.
>
>
>     Reruns do neighbour searching every frame, regardless.
>
>     Mark
>
>
>
>         On May 14, 2011, at 1:11 PM, Justin A. Lemkul wrote:
>
>
>
>             Ramachandran G wrote:
>
>                 Hello gmx users:
>                     I did 1ns simulation for my system and have the
>                 trajectory and energy files.
>                 Now i want to see the energy of some specific
>                 residues. So, i decompose(separated) the energy groups
>                 and edited the mdp file.
>                 Using the mdp file, i created a new tpr file and rerun
>                 the mdrun using the trajectory file. But when i
>                 compared the total energy between the old and new one,
>                 it differs a lot.
>                 I am doing some mistakes somewhere. Can anyone help me
>                 please. Thanks.
>
>
>             Maybe, maybe not.  Without seeing the .mdp settings and
>             the data that you're looking at, all anyone can do is
>             guess.  You also haven't stated what type of trajectory
>             (i.e. .xtc or .trr) you're using as -rerun input.  If
>             you're using an .xtc file, there is no velocity
>             information, so any property related to velocities (most
>             notably kinetic energy, but several others as well) will
>             be zero.  I suspect this is probably where the discrepancy
>             is, but it is not a problem.  Using energygrps is only
>             useful for decomposing short-range nonbonded energy terms,
>             nothing else.
>
>             -Justin
>
>             -- 
>             ========================================
>
>             Justin A. Lemkul
>             Ph.D. Candidate
>             ICTAS Doctoral Scholar
>             MILES-IGERT Trainee
>             Department of Biochemistry
>             Virginia Tech
>             Blacksburg, VA
>             jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>             <tel:%28540%29%20231-9080>
>             http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>             ========================================
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