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PAVAN RELISH DESTINY RESOLVING CRUX OF LIFE......... wrote:
I am new to Gromacs & using it with Amber force field amber03,
i am able 2 run my system of DNA till steepest descent but
when i tried to run it for cg it showed
that can not work with so much of constrains so i tried to
run it with -Dposres
Minimization with position restraints serves very little, if any, purpose in my
mind.
directly to mdrun with md integrator it showed an error
message "wrote pdb files with previous & current
co-ordinate segmentation fault."
how can i
modify my mdp file to overcome this problem ?
Your system is insufficiently minimized and/or equilibrated. Please see the
following:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
-Justin
--
========================================
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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