Try setting ntwx=1 and running for about 50 steps or so. Then take a look at
the trajectory and see if anything looks wrong. Your temperature is going up
extremely quickly given you are using the weight restraints and the langevin
thermostat. This suggests there could be something wrong with your initial
structure.
All the best
Ross
> -----Original Message-----
> From: Chris Chris [mailto:alpharecept.yahoo.com]
> Sent: Tuesday, May 08, 2012 9:23 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] help with pmemd .in file
>
> OK,
>
> I did that and it did indeed work (.out file attached), however with
> far fewer MD steps than I would have like to perform (nstlim =10). Is
> it not possible to get all 25,000 in?
>
> Here was the .in file
>
> &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=10,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=1,
> ntpr=1, ntwx=500,
> ntt=3, gamma_ln=2.0,
> tempi=0.0, temp0=300.0,
> ntr=1,
> nmropt=1
> /D
> &wt TYPE='TEMP0', istep1=0, istep2=25000,
> value1=0.1, value2=300.0, /
> &wt TYPE='END' /
> write
> 10.0
> RES 1 252
> END
> END
>
>
>
> ________________________________
> From: David A Case <case.biomaps.rutgers.edu>
> To: Chris Chris <alpharecept.yahoo.com>; AMBER Mailing List
> <amber.ambermd.org>
> Sent: Tuesday, May 8, 2012 5:15 AM
> Subject: Re: [AMBER] help with pmemd .in file
>
> On Mon, May 07, 2012, Chris Chris wrote:
> >
> > > Can someone see what I did wrong here?
> > >
> > > heat 2psj ctz first time
> > > &cntrl
> > > imin=0,irest=0,ntx=1,
> > > nstlim=25000,dt=0.002,
> > > ntc=2,ntf=2,
> > > cut=8.0, ntb=1,
> > > ntpr=500, ntwx=500,
> > > ntt=3, gamma_ln=2.0,
> > > tempi=0.0, temp0=300.0,
> > > ntr=1,
> > > nmropt=1
> > > /
>
> ..
>
> <broken_record>
> When you have problems, set nstlim=10 and ntpr=1; doesn't always help,
> but
> certainly narrows down the list of possible problems.
> </broken_record>
>
> ....dac
>
>
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Received on Tue May 08 2012 - 10:00:03 PDT
