[gmx-users] how to indicate solvent flexibility?

[Albert]

Hello Justin and Leandro:

   thanks a lot for kind advices. I am trying to us the g_msd to 
calculate the density:

first I made a index file called density.ndx with g_select, defined the 
solvent within 6A of a residue

after that I try to run g_msd with command:

g_msd_mpi -f md.xtc -s analysis.tpr -n density.ndx -mol diff_mol.xvg -o 
msd.xvg

a dialoug popped up with above command:


.....
Group 13963 (close_27926.000) has     7 elements
Group 13964 (close_27928.000) has     5 elements
Group 13965 (close_27930.000) has     7 elements
Group 13966 (close_27932.000) has     7 elements
Group 13967 (close_27934.000) has     7 elements
Group 13968 (close_27936.000) has     8 elements
Group 13969 (close_27938.000) has     9 elements
Group 13970 (close_27940.000) has     6 elements
Group 13971 (close_27942.000) has     9 elements
Group 13972 (close_27944.000) has     9 elements
Group 13973 (close_27946.000) has     9 elements
Group 13974 (close_27948.000) has    10 elements
Group 13975 (close_27950.000) has     9 elements
Group 13976 (close_27952.000) has    12 elements
Group 13977 (close_27954.000) has    10 elements
Group 13978 (close_27956.000) has     9 elements
Group 13979 (close_27958.000) has    10 elements
Group 13980 (close_27960.000) has     8 elements
Group 13981 (close_27962.000) has    10 elements
Group 13982 (close_27964.000) has    10 elements
Group 13983 (close_27966.000) has     7 elements
Group 13984 (close_27968.000) has     9 elements
Group 13985 (close_27970.000) has     8 elements
Group 13986 (close_27972.000) has     8 elements
Group 13987 (close_27974.000) has     7 elements
Group 13988 (close_27976.000) has     9 elements
Group 13989 (close_27978.000) has     6 elements
Group 13990 (close_27980.000) has     9 elements
Group 13991 (close_27982.000) has     8 elements
Group 13992 (close_27984.000) has     8 elements
Group 13993 (close_27986.000) has    11 elements
Group 13994 (close_27988.000) has    10 elements
Group 13995 (close_27990.000) has    11 elements
Group 13996 (close_27992.000) has    10 elements
Group 13997 (close_27994.000) has    11 elements
Group 13998 (close_27996.000) has    11 elements
Group 13999 (close_27998.000) has     9 elements
Group 14000 (close_28000.000) has    12 elements


I select 14000 which is the last one, but it failed with messages:

rogram g_msd_mpi, VERSION 4.5.5-dev-20121121-3e633d4
Source code file: /home/albert/software/gromacs/src/tools/gmx_msd.c, 
line: 739

Fatal error:
The index group does not consist of whole molecules
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Can't You Make This Thing Go Faster ?" (Black Crowes)


thank you very much
Albert





On 01/08/2013 06:15 PM, Justin Lemkul wrote:
>
>
> On 1/8/13 11:42 AM, Albert wrote:
>> hello:
>>
>>    I've finished a 60ns MD simulation with Gromacs and I found that the
>> flixbility of solvent molecules inside the protein is different when 
>> it binds
>> with different ligands: ie. in one case the solvent can move very 
>> fast with bulk
>> environment, and in other case the solvent forms type Hbonds with 
>> resdiues
>> inside protein.  I am just wondering how which module of Gromacs can 
>> I use to
>> indicate the solvent difference in flexibility? Is it possible to 
>> calculate the
>> entropy in certain region (let's say: 20<Z<30 ) of the solvent?
>>
>
> It sounds like g_rmsf and g_msd may be useful here.  The only way to 
> specify geometric criteria for index groups is to use g_select, but 
> then the analysis has to be done on each individual frame, not the 
> trajectory.  Dynamic selections will be more conveniently implemented 
> in a future Gromacs version.
>
> -Justin
>