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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