On 25/11/2011 6:53 PM, James Starlight wrote:
This way I've already used but is this possible to extract Gro and trp
files from uncompleated runs and not stopping this simulation ?
Copy the trajectory file. Then use trjconv on the copy however suits
you. You don't need a new .tpr, you need either the original .tpr or one
that suits your analysis.
Mark
James
2011/11/25 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
On 25/11/2011 6:38 PM, James Starlight wrote:
Mark, Tsjerk thanks!
I've check my uncompleated produced MD run by G_energy and find
that average pressure is 1.1 Bar that is most close to ref.
By the way could you tell me about extra possible ways of
checking running simmulation? ( E.g I'm calculating long produce
trajectory and want to check my uncompleated system ).
As I understood One of the possible way is the ussage of G_energy
but how I could obtain GRO and TPR file from uncompleated MD
trajectory ( .trr) (recently I've asked about this but I've
missed that topic ;o) ?
Choose a length of time in advance that you are happy to risk
being wasted. Run that length of time, make a backup, check
whatever you want to check, then continue the simulation. As you
acquire confidence, you will want to increase that time (and like
everyone you will regret that decision at least once!)
Mark
Thanks again
James
2011/11/25 Tsjerk Wassenaar <tsje...@gmail.com
<mailto:tsje...@gmail.com>>
Hi James,
There have been extensive discussions about this on the list.
Check the archives. In short, smaller systems give larger
fluctuations, and shorter simulations give larger deviations
from the expected average.
Cheers,
Tsjerk
On Nov 25, 2011 7:23 AM, "James Starlight"
<jmsstarli...@gmail.com <mailto:jmsstarli...@gmail.com>> wrote:
Dear Gromacs Users!
At the present time I'm simulating small peptide (11 a.c in
coiled conformation) in water.
I've desided to use parameters from Lysozyme simmulation (
opls ff for parametrisation and all mdp parameters from that
simulation).
Because my peptide was smaller than typical globular protein
I've desided to use bigger periodical box than in tutorial
I've used editconf -c -d 1.5 -bt cubic instead of 1.0 nm in
tutorial wich resulted in bigger box relative peptide size.
so i have this box vectors 5.39318 5.39318 5.39318
My experiment was in full agreement with the above tutorial
until NVP phase was conducted. I have conducted 100ps
equilibration but When I've checked average pressure it was
0.75 atm instead of 1 BAR and have big RMSD- 200. (also I've
checked my system visually but it looks fine- I have not
pointed any artifacts linked with unstable pressure like
voids in the solvent etc). Should I equilibrate my sustem
longer until pressure would not be stabilized to reference
BAR? What another options should i take into account during
simulation of the small peptides ?
Thanks,
James
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