[gmx-users] NPT for compressing
Elisabeth
katesedate at gmail.com
Sun May 22 04:24:53 CEST 2011
On 21 May 2011 19:02, Justin A. Lemkul <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>> 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?
BTW, by PR I meant parrinello rahman. sorry for confusion.
>
>>
>>
>>> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110521/742579d9/attachment.html>
More information about the gromacs.org_gmx-users
mailing list