Lum Nforbi wrote:
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.
This should be a very simple problem to fix. You shouldn't haphazardly change
the cutoff values. Doing so can have a very negative impact on your results.
If the smallest box vector (at the bottom of the .gro file) is less than 2 *
longest cutoff, then you are not satisfying the minimum image convention for a
periodic system. Increase the size of your system.
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.
Probably not a big deal in this case, since you just have water, but in general,
you structure file should match the topology with respect to atom names. More
complex systems can have very negative consequences when this happens.
-Justin
Thank you,
Lum
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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