[gmx-users] results of tpi

Berk Hess gmx3 at hotmail.com
Mon Aug 24 15:59:06 CEST 2009


Did you try to load the file into xmgrace?
That will give you more readable output.

I don't know what you mean with Psi.
s2 is <exp(-beta*U)>, where U is the interaction energy between the inserted
molecule and the system. V is the volume of that frame.
The entry s4 gives the average potential energy: <U exp(-beta*U)>.
The entries s5 and higher give energy components: <Ucomponent exp(-beta*U)>.


> From: Rolf.Isele at rwth-aachen.de
> To: gmx-users at gromacs.org
> Date: Mon, 24 Aug 2009 15:35:46 +0200
> Subject: [gmx-users] results of tpi
> Hi everybody,
> I'm doing calculations with results, that I receive from tpi insertions. As I don't get the results I am heading for, I starded to wonder weather I interpretate the values in the columns of the xvg file correct.
> Hear is the head of the xvg files and next to it my interpretation of its meaning
> @ s0 legend "-kT log(<Ve\S-\8b\4U\N>/<V>)"      = the total average of -kT*ln(<V*exp(-beta*Psi)>/<V>)
> /@ s1 legend "f. -kT log<e\S-\8b\4U\N>"             = -kT*ln(<exp(-beta*Psi)>)   of one frame
> @ s2 legend "f. <e\S-\8b\4U\N>"                        = <exp(-beta*Psi)> of one frame      ***
> @ s3 legend "f. V"                                             = V of one frame                              ***
> @ s4 legend "f. <Ue\S-\8b\4U\N>"                      =  no idea
> @ s5 legend "f. <U\sVdW rest\Ne\S-\8b\4U\N>"    = no idea
> The values that I need are these branded with "***". Were my suggesstions right?
> Regards, Rolf
> _______________________________________________
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

What can you do with the new Windows Live? Find out
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090824/8c641cf4/attachment.html>

More information about the gromacs.org_gmx-users mailing list