[gmx-users] position restraint and pdb

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Nov 8 15:27:04 CET 2008


> Yes. You can use GROMACS to simulate traffic if you want to. :-)

Mark, do you have a force field for that?

>> As i had done it with 4 residue with blocking group. But then i got the
>> error for rvdw and rlist as they should be nearer to cutoff value.
>> So instead of decreasing the value of rvdw. i increased my X, Y, Z
>> coordinates.
>> Tell me whether i m correct or not.
> We can't possibly tell because we don't know
> a) your objective and
> b) what sizes you've tried, and
> c) what force field you're trying to use, and
> d) what errors you've received and
> e) what other problems you've encountered.
> f) how you've tried to solve the above.

Well, probably this is due to the fact that you only use a 1.0 nm
distance from the solute to the wall, which makes the box dimension
2.0+peptide dimension, together being less than twice the cutoff
radius used (2*1.4=2.8) for at least one direction. Increasing the box
dimensions will solve the problem. If you're going to work with more
small peptides, it's good to just set the box at 3 nm or so (editconf
-f protein.gro -o out.gro -bt dodecahedron -box 3.0).



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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