pkmukher wrote:
Mark and other users,
Thanks for the input. I understand that translation does
not have any effect on the energy calculations since the
point of reference is the protein itself.
The problem over here is that if a translation operation is
to be done it should perform the same operation on all the
X,Y or Z coordinates.
That's not necessary either... (assuming PBC) each atom can undergo an
infinite variety of translations, each invariant modulo the box vectors,
and energy is invariant.
A brief summary of the job - i have a protein + peptide
system which i want to simulate. I have generated peptide
itp file using PRODRG and included in the protein .top
file. I am doing a dummy mdrun to check the system.
I have added excerpts from the structure files and the .mdp
file.The first is the input structure file for grompp > .trp
file > mdrun while the second is the output of the
mdrun.
I don't understand what you've done in these last two sentences.
Comparing the two structures whats happening is that
for the protein coordinates (till 1895) a tranlation is
being performed only on the protein X coordinates while for
the peptide the translation is being performed only on the Y
and Z coordinates. This results in the peptide and protein
to be placed separate from each other.Please help me with
your suggestions. Thanks in advance
grompp will be placing both the molecules in a periodic cell convenient
to it (with the first atom in the same cell?). We can't tell whether
this is happening sensibly unless you provide the first few atoms of
both molecules and the size of your cell.
You can play with trjconv (read the man page) on your output structure
file to see what is happening here. Be aware that your visualization
software may or may not do unexpected things to the input you give it
when PBC effects are present.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
