Hi Cynthia,
I'm also working on including some tabulated functions but I don't have
any simulation yet. Thus I'm not a 'specialist' in this topic, but I
hope I can help you a little.
Dear
all,
I tried to include 2 tabulated dihedral potential functions into
my simulation. But it seems to be not able to generate correct results.
The system just exploded. I defined 3601 points in each table (from
-180 to 180 with an increment 0.1). After 'mdrun', GOMACS generates two
warning information:
WARNING: For the 3598 non-zero entries for table 0 in
table_d1.xvg the forces deviate on average 193% from minus the
numerical derivative of the potential
WARNING: For the 3598 non-zero entries for table 0 in
table_d2.xvg the forces deviate on average 193% from minus the
numerical derivative of the potential
Do these two warnings matter very much? I checked the values for
x,f(x),-f'(x) in the tables and don't think there're mistakes. has
anyone of you met with such problems?
There're also some other confusions:
1. Can the constant k before the cubic spline function be
defined arbitrarily, as long as the multiplication of k and f(x) equals
to the dihedral potential?
2. The tables do not need to be supplied to mdrun using
'-tableb', right? I found if I omitted -tableb and the following table
files, GROMACS can still go and find the two tables.
3. how to use '-tableb' if two tables are supplied? '-tableb
table_d1.xvg table_d2.xvg' or '-tableb table_d1.xvg -tableb
table_d2.xvg'? I tried both and error information was given that
GROMACS can not find 'table_d1_d1.xvg'. I then delete '_d1' in both of
the commands and there was no error information any more. It seems that
only one table can be supplied to mdrun by using'-tableb', the second
table can not be recognized all the time.
If you read the manual page of mdrun (i.e. in the appendix of GROMACS
manual) you find the following:
"When tabulated bonded functions are present in the topology,
interaction functions are read using the -tableb option. For each
different tabulated interaction type the table file name is modified in
a different way: before the file extension an underscore is appended,
then a b for bonds, an a for angles or a d for dihedrals and finally
the table number of the interaction type."
Thus you run mdrun -tableb mytablefilename.xvg and GROMACS
automatically adds _d* before .xvg, where * is the
table number specified in the topology. In your case GROMACS finds your
table files automatically, because you gave them the default names
GROMACS searches for.
For further informations read chapters 4.2.13, 5.7.1 and D.74 (manpage
mdrun) of the GROMACS manual.
Johannes
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