[gmx-users] how to indicate solvent flexibility?

[Justin Lemkul]

On 1/10/13 4:45 AM, Albert wrote:
> 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
>

Each of these groups corresponds to the atoms that satisfied the g_select 
criteria for a given frame.  That may not continuously apply to what you 
actually want to measure.

>
> 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
> -------------------------------------------------------
>

So make an index file that contains intact molecules.  That's a prerequisite for 
using the -mol flag.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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