Hi all,
I am having an issue with the temperature after I have slowly heated up the
system:
100ps MD with res on protein
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300,
ntt = 3,
gamma_ln = 1.0,
nstlim = 50000, dt = 0.002
ntpr = 5000, ntwx = 5000, ntwr = 5000
/
Keep protein fixed with weak restraints
50.0
RES 1 40
END
END
I use the sander.MPI
mpirun -np 16 ~/amber14/bin/sander.MPI -O -i md_disulfides.in -p
solv.prmtop -c heat.rst -r md.rst
with the following md input file:
10ps MD
&cntrl
imin = 0, irest = 0, ntx = 1, iwrap=1,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,ig=-1,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300, temp0 = 300,
ntt = 3, gamma_ln = 1.0,
nstlim = 10000000, dt = 0.002,
ntpr = 5000, ntwx = 5000, ntwr = 5000
/
I do want to start from random seeds to get indenpendent runs so I set the
ig=-1 but still I would expect to be close to the equilibrated system.
but from the first round I get the following error/ warning
NSTEP = 0 TIME(PS) = 100.000 TEMP(K) = 440.42 PRESS =
-621.5
Etot = -19730.8465 EKtot = 8077.7368 EPtot =
-27808.5832
BOND = 105.8078 ANGLE = 205.4744 DIHED =
473.4839
1-4 NB = 130.7175 1-4 EEL = 2395.4889 VDWAALS =
3606.5258
EELEC = -34726.0816 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 2504.5210 VIRIAL = 4159.2641 VOLUME =
123313.0860
Density =
0.7475
Ewald error estimate: 0.6640E-04
------------------------------------------------------------------------------
***** Processor 0
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 1415 Allocated: 1412
any help appreciated - thanks!
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Received on Wed Apr 12 2017 - 22:30:02 PDT
