[gmx-users] NPT for compressing
Justin A. Lemkul
jalemkul at vt.edu
Sun May 22 04:02:27 CEST 2011
Elisabeth wrote:
>
>
>
>
> On 20 May 2011 23:04, Mark Abraham <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.
>
>
>
>> When I use constraints for all-bonds and dt of 0.002 compressing
>> the box works well and I get density of above 600 SI which is the
>> actual density of alkane. Can any one help why setting no
>> constraints and dt=0.001 leads to the error message shown above.
>
> You probably got lucky the first time and not the second. Or, your
> atom-atom bond interactions are no good.
>
>
>> When no constraints is used PR doesnt work for compressing
>
> So you want to restrain the positions of heavy atoms, but compress a
> pure system? This is contradictory. How do you want to decrease the
> volume if the atoms aren't allowed to move much?
>
> I meant
>
>
> ; Bonds
> constraints = none
>
>
> not restraining position of atoms.
>
Constraints and restraints are different.
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
You said you were using position restraints (presumably that's what "PR" means).
If this is not the case, please provide an accurate description of what you're
doing.
-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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