> On Feb 23, 2014, at 12:45 AM, richa anand <richaaanand.gmail.com> wrote:
>
> Hi,
>
> I want to do the molecular dynamics simulation between RNA-Protein
> complex. For this I have used ff12SB force field as I am using AMBER12 CUDA
> version. I have made three different input files for Heating,
> Equilibration, and Production run. The input files are given below
> respectively.
>
>
> &cntrl
> imin = 0,
> ntpr = 500, ntwr = 100000, ntwx = 500, ntwe = 500, iwrap = 1,
> ntf = 2, igb = 0,
> cut = 10.0,
> nstlim = 5000, dt = 0.002,
> tempi = 0.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0,
> ntb = 1, ntp = 0,
> ntc = 2, tol = 0.00001,
> vlimit = -1.0d0,
> /
> &ewald
> vdwmeth = 1,
> /
>
>
>
> For Equilibration the input file is:
>
>
> &cntrl
> imin = 0,
> ntx = 7, irest = 1,
> ntpr = 500, ntwr = 100000, ntwx = 500, ntwe = 500, iwrap = 1,
> ntf = 2, igb = 0,
> cut = 10.0,
> nstlim = 5000, dt = 0.002,
> tempi = 300.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0,
> ntb = 2, ntp = 1, taup = 10.0,
> ntc = 2, tol = 0.00001,
> vlimit = -1.0d0,
> /
> &ewald
> vdwmeth = 1,
> /
>
>
> For Production run the input file is:
>
> &cntrl
> imin = 0,
> ntx = 7, irest = 1,
> ntpr = 500, ntwr = 100000, ntwx = 500, ntwe = 500, iwrap = 1
> ntf = 2, igb = 0,
> cut = 10.0,
> nstlim = 5000, dt = 0.002,
> tempi = 300.0, temp0 = 300.0, ntt = 1, tautp = 10.0,
> ntb = 1, ntp = 0,
> ntc = 2, tol = 0.00001,
> vlimit = -1.0d0,
> /
> &ewald
> vdwmeth = 1,
> /
>
>
> Can I use these parameters or it needs any modification?
>
> Thanks for your consideration.
Did you try them? Did it run? If not, the error messages probably tell you what was wrong to help you fix it.
In general we can't answer "is this input file ok?" We can help debug problems as they occur but debugging input files like this without any errors (and knowing there might be no problems at all) is too time consuming and error-prone. If you had questions about one or two input variables that would be easier to help with. Also, the input file depends very strongly on what exactly you are looking to study.
There is no better substitute than trying things out yourself.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Feb 23 2014 - 08:00:02 PST
