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On 21/05/2011 10:45 AM, Elisabeth wrote:
<blockquote
cite="mid:BANLkTinO7fTwpeB1JiEcASj75pih25R=ng@mail.gmail.com"
type="cite">Dear experts,<br>
<br>
I have a box of pure hexane with density of around 50 SI (size
7nm). With the settings below I get error: <br>
<br>
vol 0.65 imb F 3% step 42100, will finish Fri May 20 18:54:05
2011<br>
Warning: 1-4 interaction between 1246 and 1249 at distance 3.580
which is larger than the 1-4 table size 2.250 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp file<br>
or with user tables increase the table size<br>
Warning: 1-4 interaction between 1249 and 1252 at distance 3.693
which is larger than the 1-4 table size 2.250 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp file<br>
or with user tables increase the table size<br>
<br>
A list of missing interactions:<br>
Bond of 2375 missing 2<br>
Angle of 4500 missing 11<br>
Ryckaert-Bell. of 5625 missing 21<br>
LJ-14 of 5625 missing 15<br>
<br>
Molecule type 'Hexane'<br>
the first 10 missing interactions, except for exclusions:<br>
Ryckaert-Bell. atoms 5 8 11 14 global 1245 1248
1251 1254<br>
LJ-14 atoms 5 14 global 1245 1254<br>
Angle atoms 8 11 14 global 1248 1251
1254<br>
Ryckaert-Bell. atoms 8 11 14 15 global 1248 1251
1254 1255<br>
Ryckaert-Bell. atoms 8 11 14 16 global 1248 1251
1254 1256<br>
Ryckaert-Bell. atoms 8 11 14 17 global 1248 1251
1254 1257<br>
LJ-14 atoms 8 15 global 1248 1255<br>
LJ-14 atoms 8 16 global 1248 1256<br>
Ryckaert-Bell. atoms 9 8 11 14 global 1249 1248
1251 1254<br>
LJ-14 atoms 9 14 global 1249 1254<br>
<br>
-------------------------------------------------------<br>
Program mdrun_mpi, VERSION 4.5.4<br>
Source code file: domdec_top.c, line: 356<br>
<br>
Fatal error:<br>
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<br>
For more information and tips for troubleshooting, please check
the GROMACS<br>
website at <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
</blockquote>
<br>
OK, your system blew up.<br>
<br>
<blockquote
cite="mid:BANLkTinO7fTwpeB1JiEcASj75pih25R=ng@mail.gmail.com"
type="cite"><br>
mdp file:<br>
<br>
; Bonds<br>
constraints = none <br>
constraint-algorithm = lincs <br>
<br>
; Run control <br>
integrator = md <br>
dt = 0.001 <br>
nsteps = 500000 ;5000 <br>
nstcomm = 100 <br>
<br>
; Output control<br>
nstenergy = 100 ; frequency to write
energies to energy file. i.e., energies and other statistical data
are stored every 10 steps<br>
nstxout = 100;1 <br>
nstvout = 0<br>
nstfout = 0<br>
nstlog = 1000 ; frequency to write
energies to log file<br>
nstxtcout = 1000 <br>
<br>
; Neighbor searching<br>
nstlist = 10 <br>
ns_type = grid <br>
<br>
; Electrostatics/VdW <br>
coulombtype = Shift <br>
vdw-type = Shift <br>
rcoulomb-switch = 0 <br>
rvdw-switch = 0.9 ;0 <br>
<br>
; Cut-offs<br>
rlist = 1.25 <br>
rcoulomb = 1.0 <br>
rvdw = 1.0 <br>
<br>
; Temperature coupling <br>
Tcoupl = v-rescale <br>
tc-grps = System <br>
tau_t = 0.1 <br>
ref_t = 300 <br>
<br>
; Pressure coupling<br>
Pcoupl = Parrinello-Rahman <br>
Pcoupltype = isotropic <br>
tau_p = 1 <br>
compressibility = 4.5e-5 4.5e-5 <br>
ref_p = 10 <br>
<br>
; Velocity generation <br>
gen_vel = yes <br>
gen_temp = 300.0 <br>
gen_seed = 173529 <br>
</blockquote>
<br>
Generating velocities and compressing from an unequilibrated initial
conformation in the same run is asking for trouble, and sometimes
you're observing it. See <a
href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation">http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a>.
Equilibrate first. Then slowly change the conditions so that you're
never all that far from equilibrium, and reach your destination.<br>
<br>
<blockquote
cite="mid:BANLkTinO7fTwpeB1JiEcASj75pih25R=ng@mail.gmail.com"
type="cite">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. </blockquote>
<br>
You probably got lucky the first time and not the second. Or, your
atom-atom bond interactions are no good.<br>
<br>
<blockquote
cite="mid:BANLkTinO7fTwpeB1JiEcASj75pih25R=ng@mail.gmail.com"
type="cite">When no constraints is used PR doesnt work for
compressing</blockquote>
<br>
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?<br>
<br>
<blockquote
cite="mid:BANLkTinO7fTwpeB1JiEcASj75pih25R=ng@mail.gmail.com"
type="cite">and berendsen gives desired densty only for high
pressures above 50 bar. I need to study my system at different
pressures from 10 bar... please comment on this.. Thanks.<br>
<br>
<p class="MsoNormal"><span style="">10 bar</span></p>
<p class="MsoNormal" style=""><span style="font-family:
"Courier New";">;<span style=""> </span>Pressure
coupling</span></p>
<p class="MsoNormal" style=""><span style="font-family:
"Courier New";">Pcoupl<span style=""> </span>=<span
style="">
</span>berendsen</span></p>
<p class="MsoNormal" style=""><span style="font-family:
"Courier New";">Pcoupltype<span style=""> </span><span
style=""> </span>=<span style="">
</span>isotropic<span style=""> </span><span
style=""> </span></span></p>
<p class="MsoNormal" style=""><span style="font-family:
"Courier New";">tau_p<span style=""> </span>=
<b style=""><span style=""> </span>0.1 </b><span style="">
</span>0.5<span style=""> </span><span style=""> </span><span
style=""> </span></span></p>
<p class="MsoNormal" style=""><span style="font-family:
"Courier New";">compressibility<span style=""> </span>=<span
style="">
</span>4.5e-5 4.5e-5<span style=""> </span> </span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">ref_p<span style=""> </span>=<span
style=""> </span>10<span style=""> </span>10<span
style=""> </span></span><span style=""></span></p>
<p class="MsoNormal"><span style=""> </span></p>
<p class="MsoNormal"><span style="">does not compress!
With and without constr.</span></p>
</blockquote>
<br>
We can't tell.<br>
<br>
Mark<br>
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