Dear Dr. A. Horn and D.A Case,
Thank you both for your valuable advice,
Well, I restarted the simulation again by putting the command "pmemd.cuda
-O -i Prod.in -o Prod.out -p POPC1.prmtop -c Prod.rst -inf Prod.mdinfo -r
Prod1.rst -x Prod1.nc", where the Prod.rst is coordinate file generated
from the previous (crashed) simulation, while the Prod1.rst and Prod1.nc
are assigned to be generated as the new/updated coordinates and trajectory
files, respectively, in the restrated simulation. The job restarted
successfully but stopped/crashed again after some time. Would you please
let me know how I can find the reason for this crash? Also, the above
mentioned command line correct or wrong to restart a crashed job?
Details of my simulation system: I have generated a POPC (80 x 80) lipid
bilayer membrane by VMD and then followed the Amber tutorial (An Amber
Lipid Force Field Tutorial (ambermd.org)
<
https://ambermd.org/tutorials/advanced/tutorial16/index.php>) to
equilibrate this POPC membrane for 400 ns prior to protein insertion (as
the literature suggested). The Prod.in and Prod1.mdinfo are given right
here for your kind information.
Your guidance could really help me to fix this issue.
TIA
Amir
Lipid production 300K 400ns
&cntrl
imin=0,
ntx=5,
irest=1,
ntc=2,
ntf=2,
tol=0.0000001,
nstlim=200000000,
ntt=3,
gamma_ln=1.0,
temp0=300.0,
ntpr=10000,
ntwr=500000,
ntwx=10000,
dt=0.002,
ig=-1,
ntb=2,
ntp=2,
cut=10.0,
ioutfm=1,
ntxo=2,
barostat=2,
/
Prod1.mdinfo
NSTEP = 6940000 TIME(PS) = 27985.000 TEMP(K) = 298.56 PRESS =
0.0
Etot = -79164.8997 EKtot = 23897.0117 EPtot =
-103061.9115
BOND = 1005.2689 ANGLE = 4191.7907 DIHED =
2532.8419
1-4 NB = 872.1375 1-4 EEL = -1216.1562 VDWAALS =
11383.3811
EELEC = -121831.1753 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
383289.1295
Density =
0.9957
------------------------------------------------------------------------------
| Current Timing Info
| -------------------
| Total steps : 200000000 | Completed : 6940000 | Remaining : 193060000
|
| Average timings for last 110000 steps:
| Elapsed(s) = 64.97 Per Step(ms) = 0.59
| ns/day = 292.58 seconds/ns = 295.31
|
| Average timings for all steps:
| Elapsed(s) = 4069.51 Per Step(ms) = 0.59
| ns/day = 294.69 seconds/ns = 293.19
|
|
| Estimated time remaining: 31.4 hours.
------------------------------------------------------------------------------
On Tue, Jun 15, 2021 at 10:05 PM David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Jun 15, 2021, Amir Zeb wrote:
> >
> >I need help to know how can I restart the md run from a
> >pre-mature terminated run?
>
> Depending on your input parameters, it is likely that there will be an
> intermediate restart file written. You can use that to re-start. Of
> course, you may see the same problem again -- depends on what caused the
> early termination of the program.
>
> ....dac
>
>
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Received on Tue Jun 15 2021 - 18:30:02 PDT
