AMBER Archive (2008)

Subject: Re: AMBER: hybrid remd imaging

From: Geoff Wood (geoffrey.wood_at_epfl.ch)
Date: Mon Mar 24 2008 - 11:16:25 CDT

Dear Carlos,

Below are the two mdin files corresponding to one particular replica.

  &cntrl
   imin = 0, irest = 1, ntx = 7,
   ntb = 1, ntp = 0,
   taup = 2.0, tol=0.0000001,
   cut = 10, ntr = 0,
   ntc = 2, ntf = 1,
   ntt = 3, gamma_ln = 1.0,
   repcrd=0, numexchg=2000, numwatkeep=350,
   nstlim = 1000, dt = 0.002, ioutfm=1,
   ntpr = 500, ntwx = 500, ntwr = 1000
   tempi = 0.0, temp0 = 300.0,
  &end
  &ewald
  &end

  &cntrl
   imin = 0, irest = 0, ntx = 1,
   ntb = 0, tol=0.0000001,
   igb=1,
   cut = 99., ntr = 0,
   ntc = 2, ntf = 2,
   tempi = 0.0, temp0 = 300.0,
   ntt = 3, gamma_ln = 1.0,
   repcrd=0, numexchg=2000, numwatkeep=350,
   nstlim = 1, dt = 0.001, ioutfm=1,
   ntpr = 1, ntwx = 1, ntwr = 1
   &end

Geoffrey Wood
Ecole Polytechnique Fédérale de Lausanne
SB - ISIC - LCBC
BCH 4108
CH - 1015 Lausanne

On Mar 24, 2008, at 4:59 PM, Carlos Simmerling wrote:

> you're right, that doesn't seem to be working correctly.
> can you send me directly your sander input? also do you have
> anything else in the system except the 1 peptide and water?
>
> On Mon, Mar 24, 2008 at 11:51 AM, Geoff Wood <geoffrey.wood_at_epfl.ch>
> wrote:
> Dear Amber Community,
>
> I am curious about the imaging done in hybrid remd calculations.
>
> If I use ptraj commands (see below) to post process a trajectory
> then the imaged trajectory looks like what one would expect (see
> attached picture).
> However, if I look at the stripped restart file then the imaging
> seems to be a bit strange (see the other attached picture). Could
> anyone comment on this?
>
>
> ptraj commands:
>
> trajin coords
> center * mass origin
> image origin center
> solvent byname WAT TIP3
> closest 350 :mask first
> trajout coords.strip nobox
>
> Thanks,
>
> Dr Geoffrey Wood
> Ecole Polytechnique Fédérale de Lausanne
> SB - ISIC - LCBC
> BCH 4108
> CH - 1015 Lausanne
> <ptrajout.jpeg><sanderRestart.jpeg>
>
>
>
>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================

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