> Date: Sat, 25 Feb 2012 09:33:37 -0500
> From: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] md sticking!
>
> On Sat, Feb 25, 2012, amir abbasi wrote:
> >
> > When I'm running a simulation in explicit water,I have face an unusual thing.
> > My system sticking in a step of simulation and not going forward.
> > what is cause this problem?
> > My Input File:
> > initial relaxation of 5nt ribozyme
> > &cntrl
> > imin = 0,irest =1, ntx = 7,
> > tempi = 300.0, temp0 = 300.0,
> > ntp = 1,
> > ntt = 3, gamma_ln =1,
> > ntb = 2,
> > ntc = 2, ntf = 2,
> > nstlim = 10000000,dt = 0.002,
> > ntpr = 100, ntwx = 100, ntwr = 1000,
> > cut = 12
> > /
>
> There is nothing obviously wrong with the above input, although using a cutoff
> of 12 is unusally large (and expensive), probably for no gain in accuracy.
>
> You don't say when it "sticks", or what partial output you received. I'd
> suggest reducing nstlim by 5 orders of magnitude, setting ntpr=1, and trying
> again. If that works, you can slowly increase the number of steps and try to
> debug.
>
> [I'm really guessing here, since you gave so little information! You have
> irest=1, so I'm assuming that you have some previous runs that worked, and
> that the system has been equilibrated, otherwise it would not make much sense
> to request a 20 ns run. Asking for 10 million steps is something that only
> makes sense when you are pretty sure that everything is fine with your system,
> which is not the case here.]
>
> ....dac
>
>
Thanks, I have run 2 stages of minimization before.
In first stage , I have restraint my molecule and equilibriate the solvent and ions with this input(as mentioned in Amber first tutorial) :
&cntrl
imin = 1,
maxcyc = 1000,
ncyc = 500,
ntb = 1,
ntr = 1,
ntc =2,ntf =2,
restraintmask = ':1-5'
restraint_wt = 500
cut = 16.0
/
then in second stage have equilibrate whole of system molecules by this input:
&cntrl
imin = 1,
maxcyc = 2500,
ncyc = 1000,
ntb = 1,
ntr = 0,
cut = 16.0
/
After those,I've run first stage of MD equilibration by this input:
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 12.0,
ntr = 1,
restraintmask = ':1-5' ,
restraint_wt = 5,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 20000, dt = 0.002
ntpr = 100, ntwx = 100, ntwr = 1000
/
and the Last stage of equilibration process this input file:
&cntrl
imin = 0,irest = 1, ntx = 7,
tempi = 300.0, temp0 = 300.0,tautp = 1.0,
ntp = 1, pres0 = 1,taup = 5,
ntt = 3, gamma_ln =1,
ntb = 2,
ntc = 2, ntf = 2,
nstlim = 30000,dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000,
cut = 12
/
In some cases of simulation,sticking occurred in the last stage of equilibration as occurred in main MD simulation as mentioned in the first message.
With Great Thanks To Dr. Case
Amir
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Received on Sat Feb 25 2012 - 08:00:01 PST
