Thank you very much
On 10/06/2017, wrote:
> I run md simulation of 10ns, and I want to restart another 10ns to
> make 20ns using below file (prod.in) and commands. Please am I right
> to proceed the process of restarting
>
> 10ns MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10.0, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 5000000, dt = 0.002,
> ntpr = 5000, ntwx = 5000, ntwr = 5000
> /
> sander.MPI -O -i prod.in -o prod.out -p ds135.prmtop -c heat.rst -r
> prod.rst -x prod.mdcrd -ref heat.rst
>
>
> You can now use prod.rst file to produce another 10ns simulation by using,
>
> sander.MPI -O -i prod.in -o prod1.out -p ds135.prmtop -c prod.rst -r
> prod1.rst -x prod1.mdcrd
>
>
>
> and then you can further combine the two trajectories to get 20ns in one
> file. Plus ntr=0 in your input file, so you dont need to put -ref in the
> end.
>
>
> Hope this helps,
>
>
> SM
>
>
> ________________________________
> From: Mustafa Alhaji Isa <mustafaisa.unimaid.edu.ng>
> Sent: Saturday, June 10, 2017 11:48:55 AM
> To: AMBER Mailing List
> Subject: [AMBER] How restart md simulation
>
> Hello
>
> I run md simulation of 10ns, and I want to restart another 10ns to
> make 20ns using below file (prod.in) and commands. Please am I right
> to proceed the process of restarting
>
> 10ns MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10.0, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 5000000, dt = 0.002,
> ntpr = 5000, ntwx = 5000, ntwr = 5000
> /
>
> sander.MPI -O -i prod.in -o prod.out -p ds135.prmtop -c heat.rst -r
> prod.rst -x prod.mdcrd -ref heat.rst
>
>
> --
> Warm regards
>
>
> Mustafa Alhaji Isa
> Bioinformatics and Computational BIology Lab,
> Department of Biotechnology,
> School of Engineering and Technology
> Sharda University
> Greater Noida, Delhi, India
> Mob No.: +918800621829
>
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--
Warm regards
Mustafa Alhaji Isa
PhD Scholar
Bioinformatics and Computational BIology Lab,
Department of Biotechnology,
School of Engineering and Technology
Sharda University
Greater Noida, Delhi, India
Mob No.: +918800621829
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Received on Sat Jun 10 2017 - 05:30:03 PDT
