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.abra...@anu.edu.au
<mailto:mark.abra...@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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