vidhya sankar wrote:
Thanks Justin,
now i have different problem when i run mdrun_d
programme with the following command
./mdrun_d -s 1HHO_md.tpr -o 1HHO_md.trr -c 1HHO_md.gro -e md.edr -nt 1
i got error as follows
Step 0, time 0 (ps) LINCS WARNING
LINCS warnings that occur immediately are almost invariably the result of a poor
starting configuration. Better energy minimization and/or equilibration are
likely necessary.
Another consideration is whether or not these groups:
tc-grps = HEM AL OXY ; two coupling groups - more accurate
are large enough to justify setting them separately. Small groups can be
unstable by themselves. Hence why one does not, for example, couple ions
separately from solvent.
-Justin
--
========================================
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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