AMBER Archive (2007)

Subject: Re: AMBER: Thermodynamic Integration with Explicit Solvent

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Tue Oct 09 2007 - 20:09:14 CDT

Thomas,

Thank you for the clarification. I followed your instructions and the
restart files show 109.4712190 in the x, y, and z positions. I can provide
you output and restart files if you wish to verify the error though I have
triple checked it. Maybe this is a small bug with the TI module? Has
anyone else had success with explicit solvent thermodynamic integration runs
using the AMBER 9 method?

Scott

On 10/9/07, Thomas Steinbrecher <steinbrt_at_scripps.edu> wrote:
>
> Hi Scott,
>
> the error you mention indicates that your prmtop is set for a trucated
> octahedron solvent box, while your rst file is for a rectangular
> box. Check its last line, the 4th-6th number, indictaing the box angles,
> should be 90.0 degrees for a rectangular and 109.47 for an octahedral
> box. Why you only get this error in a TI run is strange however, it should
> occur in regular MD, too.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
>
> On Tue, 9 Oct 2007, Scott Pendley wrote:
>
> > Hello AMBER users,
> >
> > I have had a long history of using thermodynamic integration under AMBER
> 7
> > using parmtops and perturbed parmtops. I have read through Ross' AMBER
> 9
> > tutorial and I am trying to modify his implicit solvent tutorial to
> handle
> > my explicit solvent needs but I am having trouble getting it to work.
> >
> > First I attempted to using an TI input that worked well for me before
> with
> > AMBER 7
> >
> > &cntrl
> > ntr=0,
> > nstlim=3000000, nscm=2000, ntave=5000,
> > ntx=7, irest=1, ntb=1, ntpr=100,
> > ntp=0, taup=2.0,
> > dt=0.001, nrespa=2,
> > ntt=0, temp0 = 300., tautp=2.0,
> > ntc=2, ntf=2, tol=0.000001,
> > ntwr = 10000, ntwx=0, klambda=6,
> > icfe=1, clambda=0.043882786,
> > cut=9.0,
> > /
> >
> > This unfortunately, led to errors with values exceeding the vmax. Next
> I
> > tried to modify Ross' input to allow for explicit solvent and am using
> >
> > &cntrl
> > nstlim =3000000, nscm=2000,
> > ntx=1, irest=0, ntpr=1000,
> > tempi=300.0, temp0=300.0, ntt=3, gamma_ln=5.0,
> > ntb=0, igb=0, cut=9.0,
> > dt=0.001,
> > ntc=2, ntf=2,
> > ntwr = 10000, ntwx=1000, ntave=5000
> > icfe=1, clambda=0.0034357, klambda=6,
> > /
> >
> > This leads to a very strange error "Error: ifbox=2 in prmtop but angles
> are
> > not correct". I have tried the parmtop and coordinate files with a
> regular
> > MD input and they seem fine. If others have had success could they
> share
> > their input file with me or any suggestions that can help me further
> along
> > this way.
> >
> > Thank you,
> >
> > Scott
> >
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