[gmx-users] Conversion codes
gia at chem.unr.edu
Fri Sep 30 19:11:02 CEST 2005
Phuong and Erik,
Thanks for your answers. As I mentioned my question was not related to
Gromacs. The point is that we do MD simulation for unimolecular reactions,
first we fit potential energy surface (PES) by interpolating fitting method
developed in our group and then do trajectory calculations. Instead of doing
ab initio calculations to generate data points we use other analytical
methods for data points (we save a time). In this case we have the PES for
five-atomic molecule obtained from one of the analytical potential programs,
and coordinates are cartesian. Our fitting code is written in interatomic
distances (for some reasons interatomic distances are the best). I agree
with you Erik, if number of atoms is more than four we have a redundancy in
This is all, why I needed this conversion.
I apologize for taking your time.
----- Original Message -----
From: "Erik Lindahl" <lindahl at sbc.su.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Friday, September 30, 2005 12:33 AM
Subject: Re: [gmx-users] Conversion codes
> Hi Gia,
> I'm not quite sure what you're after - vec.h contains all the stuff you
> need for distances/angles/torsions, or did you think of some sort of
> matrix representation of _all_ interatomic pair distances? One problem is
> of course that such a matrix would over-determine the system.
> On Sep 30, 2005, at 8:51 AM, gia at chem.unr.edu wrote:
>> I was wondering if anyone knows the conversion codes, which converts
>> coordinates to interatomic (not internal) distances. I know this
>> question is
>> not related directly to Gromacs, but I would appreciate any answer on
>> Thanks in advance,
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>> gmx-users at gromacs.org
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