Hello everyone,
Thanks to Tsjerk, Mark Abraham, Justin and Dr. Vitaly for the very
useful inputs to my quest for generating a .gro file from a .pdb file.
I am now trying to minimize the energy of the system so I can do an
mdrun but I keep having the error message:
the cut-off length is longer than half the shortest box vector or longer
than the smallest box diagonal element. Increase the box size or decrease
rlist.
I have changed the values of rlist, rvdw and rcoulomb, and even the
box size several times but I still keep having this message. Please, I need
help to figure out what to do to fix this problem.
The command line I am using is:grompp -f waters.mdp -c waters_b.gro -p
water.top -o watersinput.tpr
Also, is there a way to convert atom types from one format to another?
I also have the following warnings:
"Warning: atom name 1 in water.top and waters_b.gro does not match (OW - O)
Warning: atom name 2 in water.top and waters_b.gro does not match (HW1 - H)
Warning: atom name 3 in water.top and waters_b.gro does not match (HW2 - H)
atom names from water.top will be used
atom names from waters_b.gro will be ignored."
I had drawn my molecule in ghemical and exported as a pdb file and so the
atom types O and H were automatically generated.
Thank you,
Lum
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