[gmx-users] Deuterium order parametr

Parthasarathi, Ramya ramyasarati at ou.edu
Mon Sep 5 19:51:05 CEST 2011

Sorry did not send the email.. was sent by mistake due to some error in the mail box. I apologise..

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Monday, September 05, 2011 12:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Deuterium order parametr

Parthasarathi, Ramya wrote:
> Hi,
> I am trying to write a code for Deuterium order parameter of DOPC lipid. 
> I went through the code in gmx_order.c, I did the following,
> 1.       I took the carbons in the chain, and found its neighbors.
> 2.       Took the bilayer normal and found the angle between the bilayer 
> normal and the -CH molecular axis.
> 3.       Took care of the periodic boundary conditions since I use NPT 
> ensemble.
> But the code in gmx_order.c in GROMACS tries to do a lot of things other 
> than this, as I don't know C or C++ language that it is using, I don't 
> know what else I am supposed to include.
> Can someone please help me?

My last reply should have given you some indication that your code is wrong, but 
the purpose of this list is not to critique your coding or teach you how to 
write programs.  You've not given any real specifics on what you're doing aside 
from a basic outline that suggests the overall workflow is correct.  The end 
result, however, is not, and that's all anyone can tell.  You'd be best served 
trying to learn how g_order works, or otherwise find suitable code in a language 
with which you are familiar.



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

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