On 9/27/12 12:04 PM, Paula Andrea Delgado Pinzon wrote:
Hello gromacs users,
I am doing energy minimization of a big protein with distance restraint (i need
to create interactions between a group of residues, so i need them to be
close), but in the resultant pdb a don't see those residues close, so how can I
verify that the distance restraint are working?. Another unrelated question, is
that i am doing the simulation in vacumm, also in this case i need to
neutralized the system?, because with the command genion i need solvent to
replace by ions, so in this case i can't do that part.
There should be a distance restraint energy term printed to the .log file when
using distance restraints. If you need help troubleshooting, we will need to
see your topology section specifying the [distance_restraints] and your .mdp file.
For simple energy minimization, your outcome is probably not going to be heavily
impacted by net charge. If you plan on conducting any simulations in vacuo,
refer to the considerable literature on this topic for methodology.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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