Dongsheng Zhang wrote:
Yang Ye,
I am sorry to tell you I am not clear yet. Do you think I need to
specify energygrps and corresponding energygrp_table?
If so, then I got any error message. gp1 includes atom A, and gp3
includes atom A and B. Gromacs will complain that atoma has been in two
groups. Each group uses it own different table, but the group members
are overlapping bwteen some groups. How can I fix it?
You don't need to define 1-4 group again. with -table and -tablep for
mdrun, between energy group A and B, 1-2 interaction will be looked up
from table_A_B.xvg and 1-4 interaction will be looked up from
tablep_A_B.xvg.
And also, energygrps shall corresponds to energygrp_table.
So, instead to have
energygrps = gp1 gp2 gp3 gp4 gp5 gp6 ... gp12
energygrp_table = A A B B C C A B A C B C A14 A14 B14 B14 C14 C14 A14
B14 A14 C14 B14 C14
You shall have
energygrps = A B C ...
energygrp_table = A A B B C C A B A C B C
If not, I really have concern how gromacs knows to look for
table_A_A.xvg when it calculates A-A nonbonded interaction and look for
table_A14_A14.xvg when it calculates 1-4 interaction between A and A
monomers.
Could you please give me more instruction? Thank you for your help!
Dongsheng
On Wed, 2006-07-12 at 11:18 +0800, Yang Ye wrote:
Don't worry about that.
mdrun -tablep {tablep} will follow the scheme {tablep}_A_A.xvg,
{tablep}_B_B.xvg ...
{tablep} may be replaced by your own filename.
Yang Ye
Dongsheng Zhang wrote:
Yang ye,
Thank you very much.
I have three different monomers in my system, so I have 6 different
regular VMDs and 6 different 1-4 interactions. Could you please tell me
how to organize those table.xvg files?
energygrps = gp1 gp2 gp3 gp4 gp5 gp6 ... gp12
energygrp_table = A A B B C C A B A C B C A14 A14 B14 B14 C14 C14 A14
B14 A14 C14 B14 C14
If I set as the above, I wonder how gromacs know the last 6 table is for
1-4 interaction.
All the best!
Dongsheng
On Wed, 2006-07-12 at 09:54 +0800, Yang Ye wrote:
mdrun -tablep
Dongsheng Zhang wrote:
Hello, GMX users,
I have a coarse-grained model. Both 1-4 and regular vdw interaction are
tabulated, but no electrostatic interaction. Since there is no entry for
1-4 interaction in energy_table. I am thinking to fool gromacs by
treating 1-4 interactions as electrostatic interactions, in other words,
every time when 1-4 interaction energy needed, I will ask gromacs to
calculate COUL energy by reading energy_table. Does anyone know where
1-4 interaction is calculated and how I can switch it to calculate COUL
energy in the source code? Any help will be highly appreciated!
All the best!
Dongsheng
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