Nidhi Katyal wrote:
yes acf 14477/14477 .
I believe what Erik has been asking is if you have plotted the ACF curve that
g_hbond produces to see if there is any anomalous behavior.
But rmsd plot did give indication about the convergence.
What RMSD plot?
-Justin
Thank you in advance.
On Fri, Mar 30, 2012 at 4:26 AM, Erik Marklund <[email protected]
<mailto:[email protected]>> wrote:
Ah. -666 is used whenever the sitting of the kinetic model fails to
converge. This is a poor way of signalling that something went wrong
that should be changed. Again, did you *look* at the acf?
Erik
30 mar 2012 kl. 11.53 skrev Nidhi Katyal:
for another system (at 250K) also i have calculated hydrogen bond
lifetime using:
hbond -f *.xtc -s *.tpr -ac *.xvg -num *.xvg -life *.xvg -temp 250
whose output is :
acf 14477/14477
normalization for c(t)=0.0135742 for gh(t)=6.78702e-05
hydogen bond thermodynamics at T=250K
fitting parameters chi^2 = 3.89447e-06
Type rate time DG chi^2
forward -1.201 -0.833 -666.000 3.89447e-06
backward -0.354 -2.823 -666.000
......
Here again i am getting negative hydrogen bond lifetime.
Please suggest me where i am getting wrong and what does negative
lifetime mean?
Thank you in advance.
On Thu, Mar 29, 2012 at 12:56 PM, Erik Marklund
<[email protected] <mailto:[email protected]>> wrote:
29 mar 2012 kl. 18.47 skrev Nidhi Katyal:
Dear All
I would like to know the strength of the given bond by
calculating the lifetime of that bond.For the same reason i used:
g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg
-life *.xvg
and i got:
Type Rate(1/ps) Time(ps) ...
Forward -0.182 -5.495
.......
HB lifetime=50.60ps
Note that the lifetime obtained in this manner is close to
useless.Use the -ac option instead and check the forward
lifetime.
..
Will it be correct to say that lifetime is -5.495ps (looking
at forward time)? But then what does negative lifetime implies?
Thanks in advance.
Seems weird. Could the amount of underlying data be
insufficient? Have you looked at the acf?
Erik
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Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 6688 fax: +46 18 511 755
[email protected] <mailto:[email protected]>
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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