[gmx-users] g_clustsize

[Vitaly Chaban]

DvdS> Actually the text is incorrect (even the English is weird). If you use
DvdS> the -mol flag the program will tell you that the index file is ignored.
DvdS> If I recall correctly this wasn't always the case, and you could select
DvdS> a subset of the molecules for this analysis. No clue why that disappeared.

Yeah, without the possibility to select the groups to cluster there is
no use of the '-mol' key in most cases because in the usual liquid the distances
between particles are small enough and all the system appears to be
one huge cluster... :)


I just tried the same with gmx-3.3.1 but I broke with the following
error:

Program g_clustsize, VERSION 3.3.1
Source code file: smalloc.c, line: 113
Fatal error:
calloc for block->index (nelem=1069438469, elsize=4, file tpxio.c, line 906)
-------------------------------------------------------
"Once Again Let Me Do This" (Urban Dance Squad)
: Cannot allocate memory



DvdS> Vitaly Chaban wrote:
>> RF> In this case, you topology is read from the .tpr file and all of the 
>> molecules there are taken into account for clustering.
>> 
>> 
>> I think you are right but the following text from the g_clustsize help 
>> message has confused me:
>> 
>> 
>> "
>> 
>> When the -mol option is given clusters will be made out of molecules rather
>> 
>> than atoms, which allows clustering of large molecules. In this case an 
>> index
>> 
>> file would still contain atom numbers or your calculcation will die with a
>> 
>> SEGV.
>> 
>> "
>> 
>> 
>> So what is the sense to make index.ndx if ALL molecules are used for the 
>> calculation always...

DvdS> Actually the text is incorrect (even the English is weird). If you use
DvdS> the -mol flag the program will tell you that the index file is ignored.
DvdS> If I recall correctly this wasn't always the case, and you could select
DvdS> a subset of the molecules for this analysis. No clue why that disappeared.

>> 
>> 
>> 
>> Vitaly
>> 



===============================
Vitaly V. Chaban, Ph.D.(ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua,vvchaban at gmail.com
skype: vvchaban, mob.: +38-097-8259698