xi zhao wrote:
dear Mr Justin A. Lemkul :
I have read your _tutorial ,it is suitable for umbrella sampling method,
it is not for SMD, wham or g_wham can not be used!_
_Thnak you!_
If you want to use SMD trajectories to calculate free energy changes, you will
need Jarzynski's inequality and a large amount of sampling. I do not think such
a method is implemented in Gromacs; you may have to write your own scripts to do
this.
-Justin
4
<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
--- *10年3月24日，周三, Justin A. Lemkul /<jalem...@vt.edu>/* 写道：
发件人: Justin A. Lemkul <jalem...@vt.edu>
主题: Re: [gmx-users] how to reconstruct potentials of mean force
through time series analysis of SMD or pulling simulations
收件人: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
日期: 2010年3月24日,周三,下午9:58
xi zhao wrote:
> Dear gromacs users:
>
> How to reconstruct potentials of mean force through time series
analysis of SMD or pulling simulations; for example, software or
script using, how to reconstruct PMF in detail?
> thank you very much!
>
http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling
-Justin
>
> 4
<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
>
>
>
-- ========================================
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
========================================
-- gmx-users mailing list gmx-users@gromacs.org
<http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@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
<http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
--
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
