<br><br><div class="gmail_quote">On 21 May 2011 19:02, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
Elisabeth wrote:<div><div></div><div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<br>
<br>
<br>
On 20 May 2011 23:04, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br>
On 21/05/2011 10:45 AM, Elisabeth wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear experts,<br>
<br>
I have a box of pure hexane with density of around 50 SI (size<br>
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<br>
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<br>
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<br>
because some atoms involved moved further apart than the<br>
multi-body cut-off distance (1.25 nm) or the two-body cut-off<br>
distance (1.25 nm), see option -rdd, for pairs and tabulated bonds<br>
also see option -ddcheck<br>
For more information and tips for troubleshooting, please check<br>
the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
</blockquote>
<br>
OK, your system blew up.<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
mdp file:<br>
<br>
; Bonds<br>
constraints = none constraint-algorithm = lincs <br>
; Run control integrator = md dt = 0.001 nsteps = 500000 ;5000 nstcomm = 100 <br>
; Output control<br>
nstenergy = 100 ; frequency to write<br>
energies to energy file. i.e., energies and other statistical data<br>
are stored every 10 steps<br>
nstxout = 100;1 nstvout = 0<br>
nstfout = 0<br>
nstlog = 1000 ; frequency to write<br>
energies to log file<br>
nstxtcout = 1000 <br>
; Neighbor searching<br>
nstlist = 10 ns_type = grid <br>
; Electrostatics/VdW<br>
coulombtype = Shift vdw-type = Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 <br>
; Cut-offs<br>
rlist = 1.25 rcoulomb = 1.0 rvdw = 1.0 <br>
; Temperature coupling Tcoupl = v-rescale tc-grps = System<br>
tau_t = 0.1 ref_t = 300 <br>
; Pressure coupling<br>
Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 compressibility = 4.5e-5 4.5e-5 ref_p = 10 <br>
; Velocity generation gen_vel = yes gen_temp = 300.0 gen_seed = 173529 <br>
</blockquote>
<br>
Generating velocities and compressing from an unequilibrated initial<br>
conformation in the same run is asking for trouble, and sometimes<br>
you're observing it. See<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation" target="_blank">http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a>.<br>
Equilibrate first. Then slowly change the conditions so that you're<br>
never all that far from equilibrium, and reach your destination.<br>
<br>
Hello Mark,<br>
<br>
My box of alkane was already equilibrated using a NVT run. I just<br>
have to increase the density.<br>
After NVT run, do I have to turn off gen_vel = yes for NPT run? Is this necessary for all NPT runs?<br>
<br>
</blockquote>
<br></div></div>
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.<div class="im">
<br>
Sorry but to double check this, for NPT I need command below? <br></div></blockquote><div><br>grompp -f md.mdp -c last-frame-from-NVT.gro -p .top -t trajectory-file- from- NVT.trr -o md-NPT.tpr<br> <br>How do I introduce checkpoint file from previous NVT run?<br>
<br>BTW, by PR I meant parrinello rahman. sorry for confusion.<br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
When I use constraints for all-bonds and dt of 0.002 compressing<br>
the box works well and I get density of above 600 SI which is the<br>
actual density of alkane. Can any one help why setting no<br>
constraints and dt=0.001 leads to the error message shown above. <br>
</blockquote>
<br>
You probably got lucky the first time and not the second. Or, your<br>
atom-atom bond interactions are no good.<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
When no constraints is used PR doesnt work for compressing<br>
</blockquote>
<br>
So you want to restrain the positions of heavy atoms, but compress a<br>
pure system? This is contradictory. How do you want to decrease the<br>
volume if the atoms aren't allowed to move much?<br>
<br>
I meant<br>
<br>
<br>
; Bonds<br>
constraints = none <br>
<br>
not restraining position of atoms.<br>
<br>
</blockquote>
<br></div>
Constraints and restraints are different.<br>
<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints" target="_blank">http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints</a><br>
<br>
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.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br><font color="#888888">
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