[gmx-users] micelle clustering

[Tsjerk Wassenaar]

Hi Sulatha,

With my clustering algorithm there can be no infinite loop :)
By the way, sorry for the error messages you ran into with compiling
4.0.7. It had escaped me that these changes were made after that
version.

Cheers,

Tsjerk

On Fri, Jul 1, 2011 at 8:29 AM, sulatha M. S <mssulatha at gmail.com> wrote:
> Thanks Mark,
> I will do the analysis in 4.5.4. Hope while doing the micelle clustering I
> will not get into a infinite loop as in 4.0.7.
> If I understand correctly, While using trjconv -pbc cluster,  I should use
> -e 0.002  or the frames (-dump option) in the xtc file  (generated after the
> micelles are formed)
>
> Sulatha
>
>
> 2011/7/1 Mark Abraham <Mark.Abraham at anu.edu.au>
>>
>> On 1/07/2011 3:35 PM, sulatha M. S wrote:
>>>
>>> Hi Tsjerk,
>>>
>>> I installed gromacs myself. I put the modified gmx_trjconv.c code in the
>>> /src/tools subdirectory where the source code is located and tried the
>>> command
>>> make trjconv
>>> But it gives me a series of error messages, as given below.
>>
>> They're all mismatches because of changes between 4.0.7 and 4.5.4
>>
>>> My gromacs version is 4.0.7. I would like to continue in this version
>>> till I finish the set of runs which I have been doing before moving into
>>> 4.5.4 version. or else can I do the analysis alone in gromacs 4.5.4 with the
>>> xtc files generated from 4.0.7 version?
>>
>> Do that. The file formats are unchanged.
>>
>> Mark
>>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands