shahid nayeem wrote:
Dear Gromacs Users
I wanted to study the interaction between a small molecule and protein.
I prepared the system by inserting small molecule -nmol and protein by
genbox and then I solvated it with water. when I tried to do PR dynamics
it started giving many LINC WARNINGS. I reduced the time
of equilibration and then PR run was completed without any warning. When
I used production run it started giving LINC warning.Even after setting
GMX_MAXCONSTRWARN to -1 I am getting LINC warning and programme
termination with fatal error. Instead of simple docking I want to do MD
with GROMACS to see interaction between the two molecule. Please suggest
me, how can I do this.
Thanking you.
Your system is physically unstable, either due to the simulation parameters
(.mdp), topology (likely of the ligand), or the initial geometry. Please
consult the following:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
If you want more useful advice, you'll have to post more useful diagnostic
information (.mdp settings, topology, etc).
-Justin
Shahid Nayeem
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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