[gmx-users] NPT for compressing
Justin A. Lemkul
jalemkul at vt.edu
Sun May 22 04:30:08 CEST 2011
Elisabeth wrote:
>
>
> On 21 May 2011 19:02, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Elisabeth wrote:
>
>
>
>
>
> On 20 May 2011 23:04, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>> wrote:
>
> On 21/05/2011 10:45 AM, Elisabeth wrote:
>
> Dear experts,
>
> I have a box of pure hexane with density of around 50 SI
> (size
> 7nm). With the settings below I get error:
>
> vol 0.65 imb F 3% step 42100, will finish Fri May 20
> 18:54:05 2011
> Warning: 1-4 interaction between 1246 and 1249 at
> distance 3.580
> which is larger than the 1-4 table size 2.250 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Warning: 1-4 interaction between 1249 and 1252 at
> distance 3.693
> which is larger than the 1-4 table size 2.250 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> A list of missing interactions:
> Bond of 2375 missing 2
> Angle of 4500 missing 11
> Ryckaert-Bell. of 5625 missing 21
> LJ-14 of 5625 missing 15
>
> Molecule type 'Hexane'
> the first 10 missing interactions, except for exclusions:
> Ryckaert-Bell. atoms 5 8 11 14 global
> 1245 1248 1251 1254
> LJ-14 atoms 5 14 global
> 1245 1254
> Angle atoms 8 11 14 global
> 1248 1251 1254
> Ryckaert-Bell. atoms 8 11 14 15 global
> 1248 1251 1254 1255
> Ryckaert-Bell. atoms 8 11 14 16 global
> 1248 1251 1254 1256
> Ryckaert-Bell. atoms 8 11 14 17 global
> 1248 1251 1254 1257
> LJ-14 atoms 8 15 global
> 1248 1255
> LJ-14 atoms 8 16 global
> 1248 1256
> Ryckaert-Bell. atoms 9 8 11 14 global
> 1249 1248 1251 1254
> LJ-14 atoms 9 14 global
> 1249 1254
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.5.4
> Source code file: domdec_top.c, line: 356
>
> Fatal error:
> 49 of the 18125 bonded interactions could not be calculated
> because some atoms involved moved further apart than the
> multi-body cut-off distance (1.25 nm) or the two-body cut-off
> distance (1.25 nm), see option -rdd, for pairs and
> tabulated bonds
> also see option -ddcheck
> For more information and tips for troubleshooting, please
> check
> the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> OK, your system blew up.
>
>
>
> mdp file:
>
> ; Bonds
> constraints = none
> constraint-algorithm = lincs
> ; Run control integrator
> = md dt =
> 0.001 nsteps = 500000 ;5000
> nstcomm = 100
>
> ; Output control
> nstenergy = 100 ; frequency
> to write
> energies to energy file. i.e., energies and other
> statistical data
> are stored every 10 steps
> nstxout = 100;1 nstvout
> = 0
> nstfout = 0
> nstlog = 1000 ; frequency
> to write
> energies to log file
> nstxtcout = 1000
> ; Neighbor searching
> nstlist = 10 ns_type
> = grid
> ; Electrostatics/VdW
> coulombtype = Shift
> vdw-type = Shift rcoulomb-switch
> = 0 rvdw-switch = 0.9 ;0
>
> ; Cut-offs
> rlist = 1.25 rcoulomb
> = 1.0 rvdw = 1.0
>
> ; Temperature coupling Tcoupl =
> v-rescale tc-grps = System
> tau_t = 0.1 ref_t = 300
> ; Pressure coupling
> Pcoupl = Parrinello-Rahman
> Pcoupltype = isotropic tau_p
> = 1 compressibility
> = 4.5e-5 4.5e-5 ref_p = 10
>
> ; Velocity generation gen_vel
> = yes gen_temp =
> 300.0 gen_seed = 173529
>
>
>
> Generating velocities and compressing from an unequilibrated
> initial
> conformation in the same run is asking for trouble, and sometimes
> you're observing it. See
>
> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation.
> Equilibrate first. Then slowly change the conditions so that
> you're
> never all that far from equilibrium, and reach your destination.
>
> Hello Mark,
>
> My box of alkane was already equilibrated using a NVT run. I just
> have to increase the density.
> After NVT run, do I have to turn off gen_vel =
> yes for NPT run? Is this necessary for all NPT runs?
>
>
> You don't re-generate velocities between simulation intervals, or
> else you destroy any semblance of an equilibrated state you achieved
> before. Proper preservation of the previous ensemble is achieved
> through grompp -t with a checkpoint file.
>
> Sorry but to double check this, for NPT I need command below?
>
>
> grompp -f md.mdp -c last-frame-from-NVT.gro -p .top -t trajectory-file-
> from- NVT.trr -o md-NPT.tpr
>
> How do I introduce checkpoint file from previous NVT run?
>
Like I said, pass the checkpoint file (.cpt) to the -t flag to preserve state
information.
> BTW, by PR I meant parrinello rahman. sorry for confusion.
OK, that makes more sense. Please avoid unnecessary abbreviations :)
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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