Hi,
Restart files can contain only coordinates, or they can contain
coordinates and velocities (see
http://ambermd.org/formats.html#restart for complete details). When
you run a minimization you are not generating any velocities which is
why the last part of your restart file contains the zeros. You
probably can't just jump into full-on MD after a simple minimization
in explicit solvent. I usually have to use some restraints on my
solute to better equilibrate the solvent, then gradually relax the
restraints. See section 5 of Tutorial B1
(
http://ambermd.org/tutorials/basic/tutorial1/) for a good example of
how to do this. Keep in mind that every system is different, and may
require more or less to properly equilibrate (just keep an eye on the
energies).
-Dan
On Wed, Oct 13, 2010 at 1:57 PM, shweta <swdata7.gmail.com> wrote:
> Dear All,
>
> In my protein two residues were missing which i added using biopolymer
> module of SYBYL.After neutralising and adding explicit solvent, when i am
> minimizing only solvent job is ok but while minimising the whole protein the
> last coordinates in my restart file are 0.00. If i am submitting the job by
> using the same restart file the job is not running, however after deleting
> the last zeroes from restart file the further job is running. But i am not
> able to achieve stable structure in equilibration step even after 1.5ns
> run.my input files are as,
>
> min1:
> initial minimization for only solvent and ios
> &cntrl
> imin = 1,
> maxcyc = 2000,
> ncyc = 500,
> ntb = 1,
> ntr = 1,
> ntr = 1,
> restraint_wt = 500.0
> restraintmask = :1-335,
> cut = 10.0
> /
> min2:
> initial minimization whole system
> &cntrl
> imin = 1,
> maxcyc = 2500,
> ncyc = 1000,
> ntb = 1,
> ntr = 0,
> cut = 10.0
> /
>
> equil: heat full-pro
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=250000,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=2, ntp=1, taup=2.0,
> ntpr=1000, ntwx=1000,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> /
>
>
> Kindly suggest me that whether non-stabilisation in equilibration step is
> due to this restart file error and how can i overcome.
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Received on Thu Oct 14 2010 - 05:30:03 PDT
