Hi,
Please send your out file (*.out) to check what possibly has gone wrong.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Garima Singh [mailto:garimabioinfo.gmail.com]
Sent: Thursday, May 04, 2017 12:19 PM
To: amber.ambermd.org
Subject: [AMBER] How to restart MD
Dear Amber users,
I am new user of AMBER to do some MD calculations and one of my runs was stopped after NSTEP = 15082000 When i restart md which was stop at
TIME(PS) = 31164.000 while in restart output file it start at NSTEP =
1000 TIME(PS) = 31167.000 what should i do for restart after this step
NSTEP = 15082000 TIME(PS) =31164.000 because when i consider NSTEP
= 1000 TIME(PS) = 31167.000 this step will complete 25000000 step and
time period increase more then 50 ns.
I am using this file for restart md
*mpirun -np 4 sander.MPI -O -i Prod.in -o Prod1.out -p cdal7.prmtop -c Prod.rst \-r Prod1.rst -x Prod1.mdcrd -inf Pro*
In Prod.in file
*Production &cntrl imin=0, ntx=5, irest=1, nstlim=25000000, dt=0.002, ntf=2, ntc=2, temp0=300.0, ntpr=1000, ntwx=1000, cut=8.0, ntb=2, ntp=1, ntt=1, tautp=1.0, ig=-1, /*
*Md stop at this step*
NSTEP = 15082000 TIME(PS) = 31164.000 TEMP(K) = 298.58 PRESS =
298.3
Etot = -32858.2594 EKtot = 6996.3337 EPtot =
-39854.5931
BOND = 197.1791 ANGLE = 525.5396 DIHED =
764.3479
1-4 NB = 245.8184 1-4 EEL = 4833.2059 VDWAALS =
7675.2453
EELEC = -54095.9292 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 3144.5490 VIRIAL = 2419.4503 VOLUME =
112597.1533
Density = 1.0575 Ewald error estimate: 0.1903E-03
-----------------------------------------------------------
-------------------
| Current Timing Info
| -------------------
| Total steps : 25000000 | Completed : 15082000 | Remaining : 9918000
|
| Average timings for last 1000 steps:
| Elapsed(s) = 69.37 Per Step(ms) = 69.37
| ns/day = 2.49 seconds/ns = 34685.01
|
| Average timings for all steps:
| Elapsed(s) = 531305.95 Per Step(ms) = 35.23
| ns/day = 4.91 seconds/ns = 17613.91
|
| Estimated time remaining: 97.1 hours.
-----------------------------------------------------------
-------------------
*After restart in output file*
NSTEP = 1000 TIME(PS) = 31167.000 TEMP(K) = 301.22 PRESS =
-176.7
Etot = -32888.6102 EKtot = 7058.1857 EPtot =
-39946.7960
BOND = 202.8293 ANGLE = 512.9867 DIHED =
754.1454
1-4 NB = 251.6292 1-4 EEL = 4866.7504 VDWAALS =
7681.7094
EELEC = -54216.8465 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 3149.1134 VIRIAL = 3581.5059 VOLUME =
113323.3978
Density = 1.0507 Ewald error estimate: 0.2970E-03
*I want to know why the simulation is restart from NSTEP=1000 while it should restart NSTEP = 15083000 .What should i do to find the exact steps and time when md complete after restart ? *
Thanks
*Regards--*
Garima Singh
AcSIR-PhD Fellow
Biotechnology Division
Central Institute Of Medicinal And Aromatic Plant CSIR-CIMAP Lucknow garimabioinfo.gmail.com
*INDIA* Please don't print this e-mail unless you really need to. Be Green !
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Received on Thu May 04 2017 - 00:30:04 PDT
