Hi ABDELATIF,
Have you checked the SK.rst file by opening it? Have you been using the
loop to run the command line inputs? I am asking this as your second
command showing "STOP PMEMD Terminated Abnormally!" twice. If that is the
case then you have to use a loop inside your script to give a long run.
*Best,*
*Satyajit Khatua*
On Mon, Jan 30, 2023 at 5:11 PM ABDELATIF MESSAOUDI <
amessaoudi.univ-batna.dz> wrote:
> Dear SATYAJIT
> thank you so much for your help. I really appreciate it!
> I still have the same problem
> my first run
>
> $ mpirun -np 2 pmemd -O -i 05_prod.in -o 05_prod.out -c cpx_04_eq_npt.rst
> -p SK.top -r SK.rst -x SK.mdcrd &
>
> $ grep Completed mdinfo
> Total steps: 75000000 | Completed: 1955000 ( 2.6%) | Remaining:
> 73045000
>
> after restart !!
>
> $ mpirun -np 2 pmemd -O -i 05_prod.in -o 06_prod.out -c SK.rst -p SK.top
> -r SK1.rst -x SK1.mdcrd &
> [1] 15478
> $
> Unit 9 Error on OPEN: SK.rst
>
>
>
> STOP PMEMD Terminated Abnormally!
>
> Unit 9 Error on OPEN: SK.rst
>
>
>
> STOP PMEMD Terminated Abnormally!
>
> [1]+ Termine 1 mpirun -np 2 pmemd -O -i 05_prod.in -o
> 06_prod.out -c SK.rst -p SK.top -r SK1.rst -x SK1.mdcrd
>
>
> Best regards
>
> Abdelatif Messaoudi
> LCMVAR, University of Batna 1
>
>
>
> Le lun. 30 janv. 2023 à 09:45, SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
> a écrit :
>
>> Hi,
>>
>> Look at the second command line input. Your -r flag is similar to the -c
>> flag. -r flag is for generating new restart for the subsequent run. Be
>> careful with that.
>>
>>
>> Best,
>> Satyajit Khatua
>>
>> Get Outlook for Android <https://aka.ms/AAb9ysg>
>> ------------------------------
>> *From:* ABDELATIF MESSAOUDI via AMBER <amber.ambermd.org>
>> *Sent:* Monday, January 30, 2023 2:00:33 PM
>> *To:* amber.ambermd.org <amber.ambermd.org>
>> *Subject:* [AMBER] How restart md simulation with amber22
>>
>> Dear AMBER users,
>>
>> I run md simulation, and I want to restart using below file (prod.in) and
>> commands.
>>
>> production NTP
>>
>> &cntrl
>>
>> imin=0, nstlim=75000000,
>>
>> dt=0.002, ntc=2, ntf=2, nrespa=1,
>>
>> ntpr=5000, ntwx=5000,
>>
>> ntt=3, temp0=310, ig=-1,
>>
>> irest=1, ntx=5,
>>
>> iwrap=1, ioutfm=1,
>>
>> ntb=2, ntp=1,
>>
>> gamma_ln=2,
>>
>> /
>>
>> mpirun -np 10 pmemd -O -i 05_prod.in -o 05_prod.out -c cpx_04_eq_npt.rst
>> -p
>> SK.top -r prod_SK.rst -x SK.mdcrd
>>
>>
>> now I use prod_SK.rst file to produce another simulation by using,
>>
>> mpirun -np 10 pmemd -O -i 05_prod.in -o 05_prod1.out -c prod_SK.rst -p
>> SK.top -r prod_SK.rst -x SK1.mdcrd
>>
>>
>> I am getting the error:
>>
>>
>> Unit 9 Error on OPEN: prod_SK.rst
>>
>>
>>
>> Please am I right to proceed the process of restarting
>>
>>
>>
>> Abdelatif Messaoudi
>>
>> LCMVAR, University of Batna 1
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Mon Jan 30 2023 - 05:30:03 PST
