NAMD failure on Berendsen pressure scheme
 
 
 
 
 - From: Vlad Cojocaru <Vlad.Cojocaru$at$mpi-bpc.mpg.de>
- Subject: NAMD failure on Berendsen pressure scheme
- Date: Wed, 30 Jul 2003 14:53:39 +0200
 
 
 
 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