[gmx-users] Conversion codes

[Gia Maisuradze]

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 
interatomic coordiates.

This is all, why I needed this conversion.

I apologize for taking your time.

Best wishes,

Gia


----- 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.
>
> Cheers,
>
> Erik
>
> On Sep 30, 2005, at 8:51 AM, gia at chem.unr.edu wrote:
>
>> Hi,
>>
>> I was wondering if anyone knows the conversion codes, which  converts 
>> cartesian
>> coordinates to interatomic (not internal) distances. I know this 
>> question is
>> not related directly to Gromacs, but I would appreciate any answer  on 
>> this
>> question.
>>
>> Thanks in advance,
>>
>> Gia
>>
>>
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