AMBER Archive (2008)

Subject: AMBER: Restarting Problem in MD Simulation

From: khuram sb (khuramsb_at_gmail.com)
Date: Fri Jul 18 2008 - 05:37:07 CDT

Hi,
I am running MD Simulation. I have done the minimization and equilibration
steps.
When I was running MD Simulation step, my Computer was restarted mistakenly.
My job was performed till 1130ps (742000 steps) out of 1500ps (not in
script form).
Form this MD Simulation the following rst file for final velocity
coordinates was generated:
b_md.rst

I was restarting it using a different named output, rst and mdcrd files,
I am giving the -c b_md.rst as an initial coordinats for the rest of the MD
Simulation process.
My input is:

1IV5 :MD2 Simulation
&cntrl
  imin = 0,
  irest = 1,
  ntx = 5,
  ntb = 0,
  pres0 = 1,
  ntp = 0,
  taup = 1,
  cut = 12,
  ntc = 1,
  ntf = 1,
  igb = 1,
  ntr = 0,
  tempi = 300.0,
  temp0 = 300.0,
  ntt = 1,
  nstlim = 258000,
  dt = 0.0015,
  ntpr = 250,
  ntwx = 250,
  ntwr = 5000
 /

 but it is showing the following error:

______________________________________________________________________
zuh_at_mcg18:~/Working/1IV5> forrtl: severe (64): input conversion error, unit
9, file /home/zuh/Working/1IV5/b_md.rst
Image PC Routine Line Source
sander 084940D7 Unknown Unknown Unknown
sander 084936F7 Unknown Unknown Unknown
sander 08454C1A Unknown Unknown Unknown
sander 08417CF8 Unknown Unknown Unknown
sander 08417993 Unknown Unknown Unknown
sander 08430B81 Unknown Unknown Unknown
sander 080EF56D Unknown Unknown Unknown
sander 080C11DA Unknown Unknown Unknown
sander 080BFF05 Unknown Unknown Unknown
sander 0804A1C1 Unknown Unknown Unknown
libc.so.6 B7DA9F9C Unknown Unknown Unknown
sander 0804A101 Unknown Unknown Unknown
__________________________________________________________

Can it be restarted from 1130ps again?
If yes than what changes should I make in my input file.

My first input file for 1500ps is given below:

1IV5 :MD2 Simulation for 1500ps
 &cntrl
  imin = 0,
  irest = 1,
  ntx = 5,
  ntb = 0,
  pres0 = 1,
  ntp = 0,
  taup = 1,
  cut = 12,
  ntc = 1,
  ntf = 1,
  igb = 1,
  ntr = 0,
  tempi = 300.0,
  temp0 = 300.0,
  ntt = 1,
  nstlim = 1000000,
  dt = 0.0015,
  ntpr = 250,
  ntwx = 250,
  ntwr = 5000
 /

This job took almost 5 days.

Thanks
Khuram SB

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