From: Xin Chen (xinchen_at_ic.sunysb.edu)
Date: Wed Apr 07 2004 - 13:45:39 CDT
Hi,
Thank you so much. Do you mean that the second run actually restarted at
1.6M based on the last coordinates file even I set the first timestep at
1.5M? But if so, the total energy should be kept as a constant, as in the
first run, the total energy is a constant after about 0.1M timestep. But in
the second run, the total energy starts from another value and then converge
to the constant value, as if it starts from time step 1. Thanks.
Sincerely yours,
Xin Chen
----- Original Message -----
From: "Brian Bennion" <brian_at_youkai.llnl.gov>
To: "Xin Chen" <xinchen_at_ic.sunysb.edu>
Cc: <namd-l_at_ks.uiuc.edu>
Sent: Wednesday, April 07, 2004 10:59 AM
Subject: Re: namd-l: Restarting problem with Langevin dynamics
> Hi
>
> Aren't you starting with a totally different restart file?
> >From your config below, it seems that you are using the last coordinates
> of the 1.6M run to start again at 1.5M, so the energies are going to be
> different for the period 1.5M-1.6M in the second run. Even though you have
> renamed the firsttimestep to 1.5M that doesn't do anything for the
> restartfile that you set to get over written every 5000 steps.
>
> Regards,
> Brian
>
>
> On Wed, 7 Apr 2004, Xin Chen wrote:
>
> > The starting seed is same as set as 12345. The total energy is almost a
> > constant for the first run at 1.5M to 1.6M timestep, while in the second
run
> > restarting at 1.5M timestep, the total energy starts from another value
and
> > then converge to the constant value, as if it starts from time step 1,
> > although I set the firsttimestep 1500000. Thanks.
> >
> > ----- Original Message -----
> > From: "Mike McCallum" <mmccallum_at_pacific.edu>
> > To: "Xin Chen" <xinchen_at_ic.sunysb.edu>
> > Sent: Tuesday, April 06, 2004 11:32 AM
> > Subject: Re: namd-l: Restarting problem with Langevin dynamics
> >
> >
> > > How different? Perhaps the starting seed is reset?
> > >
> > > Cheers,
> > >
> > > Mike
> > > On Apr 5, 2004, at 22:05, Xin Chen wrote:
> > >
> > > > Hi, all
> > > >
> > > > I used Langevin dynamics to control the temperature in the
simulation.
> > > > But
> > > > it seems that I cannot restart my simulation with it. First time, I
did
> > > > simulation to 1.6M timestep, and then I restart it from 1.5M
timestep.
> > > > The
> > > > energy results from 1.5M to 1.6M timestep for these two simulation
are
> > > > different. The force field I used is AMBER. I wonder if anyone know
> > > > why and
> > > > how to solve this problem. Thanks. The configuration files is as
> > > > follows
> > > >
> > > >
> > > > First one
> > > > ===================================================
> > > > numsteps 1600000
> > > >
> > > > # initial config
> > > > temperature 373.16
> > > > seed 12345
> > > > #rigidBonds all
> > > > # output params
> > > > #cwd ./out0
> > > > outputname botulinum_water
> > > > binaryoutput no
> > > > outputEnergies 500
> > > > outputMomenta 0
> > > > outputTiming 500
> > > > outputPressure 0
> > > > # integrator params
> > > > timestep 1.0
> > > >
> > > > # force field parameters
> > > > exclude scaled1-4
> > > > 1-4scaling 1.0
> > > > switching on
> > > > switchdist 10.0
> > > > cutoff 12.0
> > > > pairlistdist 14.0
> > > > pairlistsPerCycle 10
> > > > margin 4.0
> > > > stepspercycle 20
> > > >
> > > > langevin on # langevin dynamics
> > > > langevinFile 3bta_wat.pdb
> > > > langevinDamping 5.0 # damping coefficient of 5/ps
> > > > langevinTemp 373.16 # random noise at this level
> > > >
> > > > maximumMove 0.5
> > > >
> > > > wrapWater on # wrap water to central cell
> > > > wrapAll on # wrap other molecules too
> > > > wrapNearest off # use for non-rectangular cells
> > > >
> > > > # we are using amber force field
> > > >
> > > > amber yes
> > > > parmfile 3bta_wat.top
> > > > ambercoor 3bta_wat.crd
> > > > readexclusions no
> > > > scnb 1.0
> > > >
> > > > binaryrestart yes
> > > > DCDfile bta_wat.dcd
> > > > DCDfreq 10000
> > > > DCDUnitCell yes
> > > > velDCDfile bta_wat.vcd
> > > > velDCDfreq 20000
> > > >
> > > > restartname bta_wat
> > > > restartfreq 5000
> > > > restartsave yes
> > > >
> > > > ===================================================
> > > >
> > > > Second one:
> > > >
> > > > Same, add one line:
> > > >
> > > > firsttimestep 1500000
> > > >
> > > >
> > > > ===================================================
> > > > Sincerely yours,
> > > >
> > > > Xin Chen
> > > >
> > > >
> > > --
> > > C. Michael McCallum
> > > http://chem.cop.uop.edu/cmmccallum.html
> > > Associate Professor
> > > Department of Chemistry, UOP
> > > mmccallum .at. pacific .dot. edu (209) 946-2636 v /
> > > (209) 946-2607 fax
> > >
> > >
> > > --
> > > C. Michael McCallum
> > > http://chem.cop.uop.edu/cmmccallum.html
> > > Associate Professor
> > > Department of Chemistry, UOP
> > > mmccallum .at. pacific .dot. edu (209) 946-2636 v /
> > > (209) 946-2607 fax
> > >
> >
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>
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