Thank you very much. It worked.
Regina
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
pol...@fh.huji.ac.il wrote:
Dear Justin,
Thank you very much for your answer.
Can you please explain me what do you mean by saying "EM wasn't
sufficient". What information do you need in order be able to help?
I run EM with emtol=60 and I got the following energies:
Steepest Descents converged to Fmax < 60 in 2256 steps
Potential Energy = -1.2244622e+07
Maximum force = 4.7755444e+01 on atom 1659
Norm of force = 6.3245118e-01
This was the information I wanted to see. Without it, no one had
any idea if your EM converged reasonably.
Everything seems ok.
Indeed it does.
After that I run MD using mdp file attached and I got the following error:
Started mdrun on node 0 Tue Jun 28 00:10:12 2011
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond G96Angle Improper Dih. LJ (SR) Coulomb (SR)
6.39093e+03 9.79589e+03 3.77765e+02 -1.22386e+07 -1.82773e+03
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-1.22239e+07 1.25745e+00 -1.22239e+07 2.55766e-04 -1.14611e+03
Here's your problem. The initial temperature is ridiculously small,
indicating something has gone wrong.
Cons. rmsd ()
4.25390e-06
DD step 9 load imb.: force 3.0%
-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.3
Any reason you're using a really old version of Gromacs?
<snip>
Here's your problem. The combination of:
tcoupl = Berendsen
and
gen_vel = no
is generally not stable. You should set "gen_vel = yes" to start a
reasonable equilibration period.
-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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