[gmx-developers] [Fwd: Re: Water Kinetics]

Omer Markovitch omermar at gmail.com
Sun Sep 7 19:19:04 CEST 2008

For my protein, a native contact within 2 residues or 2 atoms is defined
according to the CSU algorithm. In other words - for each native contact, I
have its sigma - the minimum distance, taken from the PDB file.
With that sigma, I have defined, for each contact, a Lennard-Jones force. I
have added this force in the topology file.
Now, DURING the simulation, I would like to know how many of these contacts
are still intact, that is - how many contacts obey, say, to a distance of

Now, I could do this analysis by taking a trajectory file that Gromacs has
already outputed, but I think its neater if I'll do this DURING the
Meaning I want to add to the source code a function that will receive a list
of my sigma_per_contact, and will output the fraction of native contacts
that currently obey 1.5*sigma.
Additionally, I would like to print the relevant energies, so I could use
the WHAM algorithm.

You help is appreciated. Omer Markovitch.

Koby Levy research group,
Weizmann Institute of Science.

On Sun, Sep 7, 2008 at 20:01, David van der Spoel <spoel at xray.bmc.uu.se>wrote:

> Omer Markovitch wrote:
>> Thanks.
>> FYI - I was already subsribed when I tried to post, the reply I got from
>> gmx-developers-bounces at gromacs.org <mailto:
>> gmx-developers-bounces at gromacs.org>  :
>> The results of your email command are provided below. Attached is your
>> original message.
>> - Results:
>>   Ignoring non-text/plain MIME parts
>> - Unprocessed:
>>   I would your help on how to do the following:
>>   I have a 2-body interaction, which I have defined in the file
>>   "topology.top", under the tag "[ pairs ]".
>>   I would like to, during the simulation itself, to generate a new file,
>> that
>>   for each frame will tell me:
>>   (1) Fraction of intact 2-bodies. [ defining intact is not an issue; I
>> could,
>>   for example, use a geometric criterion, or something similar ].
>>   (2) Current total energy, and energy parts.
>>   Now, I am familiar with C language, and not afraid of modifying the
>> source
>>   code.
>>   ==>> I will appreciate your help with telling me in what files.c and
>> which
>>   function & variables do the coordinates and energies are stored and
>>   defined <<==
> It would be easier to help you if you defined the problem somewhat more.
>   As for the actual printing, I believe that I could simply output my stuff
>>   after the function "write_xtc_traj" is called.
>>   Your help is highly appreciated! Omer Markovitch.
>  --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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