[gmx-users] the effect of "nexcl" on the result of g_rdf

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 12 16:12:41 CEST 2009

wuxiao wrote:
> Dear GMXers,
>    I have a bit puzzle about the use of nexcl. In order to calculate the 
> intermolecular g_rdf, the tpr file obtained from a top file is provided 
> with the option -s. So the nexcl in the top file would effect the result 
> of g_rdf. Suppose the nexcl is 3, whether are the two atoms seperated by 
> 3 bonds as a pair included into the calculation of the routin g_rdf? 
> Please ensure me the truth. Thanks a lot for any reply to this post.

Exclusions apply to intramolecular interactions, so I don't see how 
intermolecular interactions would be affected.  The .tpr file is generally used 
to provide a reference structure for fitting and/or mass-weighting, since a 
plain structure file will not have masses or atom types.


> Sincerely,
> Chaofu Wu, Dr 
> ------------------------------------------------------------------------
> Messenger保护盾2.0,更安全可靠的Messenger聊天! 现在就下载! 
> <http://im.live.cn/safe/>
> ------------------------------------------------------------------------
> _______________________________________________
> 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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list