Yanmei Song wrote:
Dear Justin:
Thank you so much for your quick response.
But I still don't get it. Should I calculate the standard error manually
by using the equations A17 (in B. Hess' s paper) after I get the result
by g_analyze. And then which value I should use for the sigma?
Here is the output :
invalid fit: e.e. 15.6513 a 2.17585 tau1 28.9321 tau2 46.3966
Will use a single exponential fit for set 1
Set 1: err.est. 21.0339 a 1 tau1 15.1648 tau2 0
I really appreciate your patience and help!
When you use g_analyze -ee, you are trying to fit your data to equation A17.
Your data cannot fit this expression (hence "invalid fit"). You may have
convergence issues with your data or insufficient data to begin with, but I
don't know much about that. The single exponential fit given is (I believe)
based on the last statement made in the paper:
"When the longest correlation time, tau2, is longer than the averaging interval
and (1 - alpha)tau2 is not negligible compared to alpha*tau1, there is not
enough statistics to estimate the error. An example is given in Fig. 8."
An example of such a fit is shown in that figure.
-Justin
On Fri, Nov 20, 2009 at 3:07 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Yanmei Song wrote:
Dear Justin:
I really appreciate your response and help!
I am confusing about the result by using this method. I found in
B. Hess's paper (Appendix, JCP, 116, 2002) that " this gives a
standard error estimate for 1/eta of 29.5. "; and the error he
gives for that eta is 0.006. I thought the error should be
calculated as 1/29.5=0.034. Thank you again for your help!
The relationship is not a simple inversion as you've shown it. That
is, (standard error of 1/eta) != 1/(standard error of eta). The
standard error calculation depends on a number of factors, hence all
the math in the Appendix :) An example is given in Fig. 8 of that
paper.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
