Dear Amber users,
I am still facing the problem during NPT equilibration. Around 5500 steps,
the simulation is stopping without any error. I checked it 3 to 4 times.
For test purpose, I ran NVT with force constant 10 (200 ps) and then with
1 (200 ps) and then without restraint for 1 ns. During the long
unrestrain NVT, the job ran smoothly. As soon as I started NPT, the job
halted. For a totally different system also the simulation halted during
NPT but not during NVT.
Since there is no error message I am not able to figure out where is the
problem.
Your suggestion will be appreciated.
Sincerely,
Sunita
NPT command:
sander.MPI -O -i eq_npt.in -o eq_npt.out -p GSC_D26G_solion.prmtop -c
eq_nvt_norst.rst -r eq_npt.rst -x eq_npt.mdcrd -inf eq_npt.info
Pls have a look on my pr_npt.in file.
============pr_npt.in=============
Equilibration NPT without restraints 200ps
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2, ig = -1,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 100000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
/
&ewald
order=4,
/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 02 2020 - 03:30:03 PDT
