Dear Case
Thanks for your reply.
Did you look at the output file from the second group? both of output files
are the same.
In tutorial that I use (A9). nstlim = 25000, ntpr = 2500, and not
nstlim=10, ntpr=1.
my group file:
-O -i free_1_eq_v0_0.1.in -p free_tg_2_v0_0.1.prmtop -c
free_tg_1_min_v0_0.1.rst -o free_tg_1_eq_v0_0.1.out -x
free_tg_1_eq_v0_0.1.mdcrd -r free_tg_1_eq_v0_0.1.rst
-O -i free_1_eq_v1_0.1.in -p free_tg_2_v1_0.1.prmtop -c
free_tg_1_min_v1_0.1.rst -o free_tg_1_eq_v1_0.1.out -x
free_tg_1_eq_v1_0.1.mdcrd -r free_tg_1_eq_v1_0.1.rst
my command line:
mpirun -np 4 /home/md/amber10/bin/sander.MPI -ng 2 -groupfile
free_1_eq_0.1.group &
I want to equilibrate first at constant volume, then later at constant
pressure.
are my equilibration input files for equilibration at constant volume? if
not, how to modify those?
free_1_eq_v0_0.1
&cntrl
imin = 0, ntx = 1, irest = 0,
ntpr = 1000, ntwr = 1000, ntwx = 0,
ntf = 2, ntc = 2,
ntb = 2, cut = 10.0,
nstlim = 250000, dt = 0.002,
temp0 = 300.0, ntt = 3, gamma_ln = 5,
ntp = 1, pres0 = 1.0, taup = 0.2,
icfe = 1, clambda = 0.1,
ifsc = 0,
crgmask =""
scmask =""
/
free_1_eq_v1_0.1
&cntrl
imin = 0, ntx = 1, irest = 0,
ntpr = 1000, ntwr = 1000, ntwx = 0,
ntf = 2, ntc = 2,
ntb = 2, cut = 10.0,
nstlim = 250000, dt = 0.002,
temp0 = 300.0, ntt = 3, gamma_ln = 5,
ntp = 1, pres0 = 1.0, taup = 0.2,
icfe = 1, clambda = 0.1,
ifsc = 0,
crgmask = '.269,271,273,274,275,553,555,556,557'
scmask =""
/
Try a standard run (with ifce=0). what is yor mean? icfe?
When I use nstlim=10, ntpr=1 in input files, job stopped in NSTEP=2.
output is as follows:
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 46649.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 46649. NUM_NOSHAKE = 0 CORRECTED RNDFP = 46649.
| TOTAL # of degrees of freedom (RNDF) = 46649.
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 3144926
| TOTAL SIZE OF NONBOND LIST = 6626689
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
-6151.7
Etot = -69103.4699 EKtot = 0.0000 EPtot =
-69103.4699
BOND = 43.5638 ANGLE = 284.9209 DIHED =
548.3179
1-4 NB = 256.3398 1-4 EEL = -2154.0057 VDWAALS =
4338.2557
EELEC = -72420.8623 EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = 246.0503
EKCMT = 0.0000 VIRIAL = 39658.7211 VOLUME =
298583.2222
Density =
0.7884
Ewald error estimate: 0.9303E-03
------------------------------------------------------------------------------
NSTEP = 1 TIME(PS) = 0.002 TEMP(K) = 6.28 PRESS =
-6151.2
Etot = -68812.4221 EKtot = 291.0478 EPtot =
-69103.4699
BOND = 43.5638 ANGLE = 284.9209 DIHED =
548.3179
1-4 NB = 256.3398 1-4 EEL = -2154.0057 VDWAALS =
4338.2557
EELEC = -72420.8623 EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = 246.0503
EKCMT = 3.3746 VIRIAL = 39658.7211 VOLUME =
298583.2222
Density =
0.7884
Ewald error estimate: 0.9303E-03
------------------------------------------------------------------------------
NSTEP = 2 TIME(PS) = 0.004 TEMP(K) = 10.62 PRESS =
-6043.2
Etot = -68836.1229 EKtot = 492.2629 EPtot =
-69328.3858
BOND = 44.2209 ANGLE = 274.8030 DIHED =
547.6377
1-4 NB = 255.8509 1-4 EEL = -2155.2419 VDWAALS =
4506.3717
EELEC = -72802.0281 EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = 246.5822
EKCMT = 133.5147 VIRIAL = 38985.9105 VOLUME =
297763.9478
Density =
0.7905
Ewald error estimate: 0.9093E-03
------------------------------------------------------------------------------
Be sure to use a short simulation, say nstlim=10 and
ntpr=1. Look at the test cases that are similar to yours, and try to
slowly change their input files to yours. Should I close my input condition
gradual?
On Sun, Feb 12, 2012 at 4:15 PM, case <case.biomaps.rutgers.edu> wrote:
> On Sun, Feb 12, 2012, leila karami wrote:
> >
> > I'm doing TI.
> >
> >
> > After minimization, I run system heat up phase of a MD, the job stopped
> > without any error
> > information.
> >
>
> Did you look at the output file from the second group? There may be
> information there.
> Try a short run, nstlim=10, ntpr=1.
> Try a standard run (with ifce=0).
> You might post the command line arguments and groupfile that you used?
>
> [Aside: generally, you want to equilibrate first at constant volume, then
> later at constant pressure. But this probably isn't your problem.]
>
> ....dac
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Feb 12 2012 - 06:30:03 PST
