case wrote:
> 1) at first, I open a com.pdb file (containing protein, dna, water and
> Na+)and a trajectory file of gromacs (com.xtc)by VMD.
Are the OH distances (in the water you had a problem with) OK at this point?
> then I saved trajectory as com.mdcrd file by vmd.
Now you can edit the com.mdcrd file, find the coordinates of the troublesome
water, and see if there is a problem or not.
[The idea is to focus on this one water molecule that ends up with a bad bond
length. You will be trying to find out exactly when in the process the
problem happens. Don't worry about anything else for right now...if you solve
this problem, other problems may go away as well. In principle, the x,y,z
coordinates should not be changing, and hence the bond length as well will not
change.]
> my simulation box in gromacs is cubic with 6 nm dimension.
OK...this makes it a lot less likely that you have an imaging problem, but
make sure that the prmtop and inpcrd files you create have the correct box
information--if that is getting messed up, it could lead to the behavior you
describe.
leila wrote:
Dear Case
thanks for your reply.
> Are the OH distances (in the water you had a problem with) OK at this point?
Yes. OH distances are OK at this point.
> Now you can edit the com.mdcrd file, find the coordinates of the troublesome water, and see if there is a problem or not.
com.mdcrd file only contains alot of numbers. how can I find
coordinate of certain water molecule of com.mdcrd file and then
compare with coordinate of same water molecule of com.xtc file?
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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Received on Mon Dec 27 2010 - 10:30:02 PST
