VMD-L Mailing List

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Wed Jul 30 2003 - 11:51:49 CDT

Hi Vlad,

1. You say that you did an NVT equilibration previous to the NPT dynamics
you want to run. But there is nowhere in your script a command where you
load the velocities from the file generated during equilibration
(velocities file.vel). Why do you heat up your system if you do not use
in the end the velocities of the solvent? I do not understand why you are
going back to Temperature 100.
2. I usually also read the unit cell information from the xsc file from
the previous equilibration
extendedSystem file.xsc
3. You should be able to use a
timestep of 2fs. I am not sure what water model you are using but with
Shake/Rattle on this should work (it works for me).
4. Here is what I use for the Berendsen pressure coupling:

berendsenPressure on
berendsenPressureTarget 1.01325
berendsenPressureCompressibility 4.9e-5
berendsenPressureRelaxationTime 500
berendsenPressureFreq 1

5. I also define the other parameters (even if they are =1)
fullElectFrequency 1
nonbondedFreq 1
stepspercycle 1

6. As a general rule, if something is not working, maybe you should look
back at your heating procedure and minimization, plot out some parameters
(T, Epotential, Etotal, Evdw..etc). Read Berendsen's paper about the way
the temperature and pressure coupling works.

7. Read careful the information listed in the header of the NAMD output
file (INFO), NAMD is sensitive to the name of the variables you define in
your input file. And may read them wrong or not at all.If they are
critical your simulation will not start at all but it may be that they are
not critical for the simulation to run and still their value will be the
default one

 Hope this helps,
Ioana

On Wed, 30 Jul 2003, Vlad Cojocaru wrote:

> Dear fellows,
> If you have some experience with namd could somebody explain why this
> is happening (see error message at the bottom of the message)? I am
> using the following script:. It is a constant pressure equilibration
> using Berendsen algorithm for temp and pressure. This equilibration step
> follows after a minim and a const Vol. eq in which the temperature is
> adjusted to 300 (also with temp coupling scheme). The protocol below
> works fine in AMBER but maybe there some differences between the values
> used by the 2 programs that I didnt figure out. The first eq. at const
> Vol works fine both in Amber and Namd so I guess there is something
> about pressure here. If you want more details please let me know!.
> I would appreciate any advice. Thank you very much ,
> Vlad
>
> # *** AMBER force field *** ---------------------------------
> amber on
> parmfile rnaWI.top
> coordinates rnaWI_mdeq2.pdb.coor
> readexclusions yes
> exclude scaled1-4
> 1-4scaling 0.83333333 #=1/1.2
> scnb 2
>
> #*** approximations for nonbonded interactions ------------
> switching off
> cutoff 9
> stepspercycle 1
>
> #***equilibration parameters
> minimization off
> numsteps 10000
> timestep 1.0
>
> #***SHAKE use
> rigidbonds all
>
> #***temperature regulation for equilibration step (NPT) using
> #***temperature coupling
> temperature 100.0
> tcouple on
> tcoupletemp 300.0
> tcouplefile rnaWI_ceq2.pdb ### friction coef.=1.0
> tcouplecol B
>
>
> #***constant pressure equilibration using Berendsen bath coupling
> usegrouppressure on
> useflexiblecell on
> berendsenpressure on
> berendsenpressuretarget 1.0
> berendsenpressurecompressibility 0.0000446
> berendsenpressurerelaxationtime 500
> berendsenpressurefreq 100
>
> #***PME
> PME on
> cellBasisVector1 56.21 0 0
> cellBasisVector2 0 58.53 0
> cellBasisVector3 0 0 57.89
> cellOrigin 0 0 0
> PMEGridSizeX 50
> PMEGridSizeY 55
> PMEGridSizeZ 50
> XSTfile rnaWI_mdeq3.XST
> XSTfreq 200
>
> #***constraints (holding the solute fixed)
> constraints on
> consexp 2
> consref rnaWI_mdeq2.pdb.coor
> conskfile rnaWI_res500.pdb
> conskcol B
>
> #***outputnames
> outputname rnaWI_mdeq3.pdb
> restartname rnaWI_mdeq3.rst
> dcdfile rnaWI_mdeq3.dcd
> dcdfreq 200
> veldcdfile rnaWI_mdeq3.vel.dcd
> veldcdfreq 200
> restartfreq 200
> outputenergies 100
> outputpressure 100
> binaryoutput off
> binaryrestart off
>
>
>
> ###---error-----------------
>
> RESSURE: 300 76798.7 -40631.2 58693.1 -13378.6 29200.3 -5152.76 69223.5
> -42523.7 81493.1
> GPRESSURE: 300 76687.2 -40836.2 58854.3 -13914.7 29538.5 -4262.26
> 68552.2 -42832.5 81484.6
> ENERGY: 300 2002.7469 2400.4670 550.4454 0.0000
> -61779.2755 9089.4231 60866.5902 0.0000 31247.2457 44377.6430
> 1056.1747 62497.3627 62570.0965 185386.7344 -1757.5130 -1600.7691
> ERROR: Constraint failure in RATTLE algorithm for atom 121!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely.
> ==========================================
>
> --
> Vlad Cojocaru
> Max Planck Institute for Biophysical Chemistry
> Department: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1327
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
> home tel: ++49-551-9963204
>
>
>
>
>
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