Hello Mahdi.
I dont know if this is the problem but a harmonic constraint value of 5000
for rk2 is way too high and also, you are missing the values of the
umbrella window, something like r1=29, r2=30, r3=30, r4=31 to allow the
system to sample that space.
Hope it helps!
Rodrigo
On May 10, 2012 1:59 AM, "mehdi bagherpoor" <ms.nightsky.gmail.com> wrote:
> Dear all
>
>
> I used Umbrella Sampling in MD file.
> I used Amber10 manual(page 111&112)
>
> my MD file is:
>
> *DNA 15-mer: 8ps MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 12.0, ntr = 0 ,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 1000, dt = 0.002,
> ntpr = 100, ntwx = 100, ntwr = 1000
> jar=1,
>
> /
> &wt type= "DUMPFREQ", istep1=1 /
> &wt type="END" /
> DISANG=dist.RST
> DUMPAVE=dist_vs_t
> LISTIN=POUT
> LISTOUT=POUT*
>
> and dist.RST file is:*
>
> # Change distance between atoms 943 and 1 from 17 A to 30.0 A
> &rst iat=943,1 , r2=17., rk2 = 5000., r2a=30.0, *
>
> but output is only one line that is:
> 17.00000 17.59934 -5993.44359 0.00000
>
> But change in distance is not performed.
>
> I would appreciate your help.
> Looking forward to hearing from you.
>
> Best regards
> M.Bagherpour
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Received on Thu May 10 2012 - 08:00:03 PDT
