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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> NG HUI WEN
<br>
<b>Sent:</b> Sunday, February 19, 2012 1:19 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> Distance Restraints on Protein - possible at all?<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Dear gmxusers,
<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">I have been trying to apply distance restraints on my protein but have been unsuccessful thus far.<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">I have consulted the user forum previously and with some much-appreciated help I have managed to get my simulation (with distance restraints applied) to run. However,
the joy did not last long as the simulation crashed very quickly (after ~40-50ps).
<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Below is an account of the attempts I made. Please bear with me as it is quite lenghty. I have tried to resolve the problem (but all to no avail) by :<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">a)changing the distance restraint group from CA to backbone - in case the protein is too floppy<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">b)fc from 10000 to 1000 (default) to 0 - in order to check if the problem comes from the strenght of restraints</span><span lang="EN-GB" style="font-family:"Calibri","sans-serif";color:#1F497D">
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Below sum up what I had done:<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">1) prepare disre.itp file<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">genrestr -f posre_NVT_rep1.gro -o ca_disre.itp -disre<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">2) mdp looks:<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">title = NPT<br>
define = -DDISRES <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">integrator = md
<br>
nsteps = 500000 <br>
dt = 0.002 <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">nstxout = 50000
<br>
nstvout = 50000 <br>
nstenergy = 2500 <br>
nstlog = 500 <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">nstxtcout = 50000
<br>
continuation = yes <br>
constraint_algorithm = lincs <br>
constraints = all-bonds <br>
lincs_iter = 1 <br>
lincs_order = 4 <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">ns_type = grid
<br>
nstlist = 10 <br>
rlist = 1.2 <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">rcoulomb = 1.2
<br>
rvdw = 1.2 <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">coulombtype = PME
<br>
pme_order = 4 <br>
fourierspacing = 0.12 <br>
tcoupl = v-rescale <br>
tc-grps = Protein POPC WATER_SOL_CL <br>
tau_t = 0.1 0.1 0.1 <br>
ref_t = 310 310 310 <br>
pcoupl = Parrinello-Rahman <br>
pcoupltype = semiisotropic <br>
tau_p = 1.0 <br>
ref_p = 1.0 1.0 <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">compressibility = 4.5e-5 4.5e-5
<br>
pbc = xyz <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">DispCorr = EnerPres
<br>
gen_vel = no <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">nstcomm = 10<br>
comm-mode = Linear<br>
comm-grps = Protein_POPC WATER_SOL_CL<br>
energygrps = Protein POPC WATER_SOL_CL<br>
; DISRE parameters<br>
disre = simple<br>
disre-fc = (i)10000/ (ii)1000 / (iii) 0<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">3) top file looks like this:<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">; Include forcefield parameters<br>
#include "gromos53a6_lipid.ff/forcefield.itp"<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">;Include Protein Topology<br>
#include "A2a.itp"<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">; Include Position restraint file<br>
#ifdef DISRES<br>
#include "ca_disre.itp"<br>
#endif<br>
;<br>
#ifdef POSRES<br>
#include "posre.itp"<br>
#endif<br>
;<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">;Include POPC topology<br>
#include "popc.itp"<br>
#ifdef LIPID_POSRES<br>
#include "lipid_posre.itp"<br>
#endif<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><br>
;Include water topology<br>
#include "gromos53a6_lipid.ff/spc.itp"<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">#ifdef POSRES_WATER<br>
; Position restraint for each water oxygen<br>
[ position_restraints ]<br>
; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">#endif<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">; Include topology for ions<br>
#include "gromos53a6_lipid.ff/ions.itp"<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">[ system ]<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">; Name<br>
POPC and protein in water<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">[ molecules ]<br>
; Compound #mols<br>
Protein_chain_X 1<br>
POPC 327<br>
SOL 24767<br>
CL 11<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">4) prepare .tpr file<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">grompp -f NPT_disres.mdp -c posre_NPT_rep1.gro -n index.ndx -p merged.top -t posre_NPT_rep1.cpt -o disre.tpr<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">5) mdrun<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">mdrun-mpi -v -s disre.tpr -deffnm disre -pd<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">The following are snippets of the output and log file before the simulations blew up:<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">i)fc= 10000<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">step 21300, will finish Wed Feb 15 11:07:18 2012<br>
step 21400, will finish Wed Feb 15 11:08:38 2012<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Step 21481, time 42.962 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.007728, max 0.339710 (between atoms 9 and 11)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Step 21482, time 42.964 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.022906, max 0.865028 (between atoms 12 and 16)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
16 17 31.6 0.1212 0.1447 0.1230<br>
12 16 104.7 0.1266 0.0207 0.1530<br>
9 11 110.7 0.0878 0.0397 0.1330<br>
Wrote pdb files with previous and current coordinates<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Step 21483, time 42.966 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.009368, max 0.641094 (between atoms 9 and 11)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
1 2 33.3 0.0928 0.0961 0.1000<br>
18 20 34.2 0.1474 0.1635 0.1470<br>
16 18 60.0 0.1842 0.1310 0.1330<br>
16 17 64.8 0.1447 0.1264 0.1230<br>
14 15 30.4 0.0979 0.1525 0.1530<br>
11 15 77.5 0.2435 0.1147 0.1470<br>
11 12 34.5 0.2609 0.1633 0.1470<br>
9 11 95.3 0.0397 0.2183 0.1330<br>
Wrote pdb files with previous and current coordinates<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Step 21484, time 42.968 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.013088, max 0.518530 (between atoms 12 and 16)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
1 2 40.0 0.0961 0.0952 0.1000<br>
18 19 59.6 0.0996 0.0782 0.1000<br>
....<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">ii) fc= 1000 (default)<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">step 21200, will finish Thu Feb 16 02:22:10 2012<br>
step 21300, will finish Thu Feb 16 02:22:09 2012<br>
step 21400, will finish Thu Feb 16 02:22:07 2012<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Step 21481, time 42.962 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.007728, max 0.339710 (between atoms 9 and 11)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Step 21482, time 42.964 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.022906, max 0.865028 (between atoms 12 and 16)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
16 17 31.6 0.1212 0.1447 0.1230<br>
12 16 104.7 0.1266 0.0207 0.1530<br>
9 11 110.7 0.0878 0.0397 0.1330<br>
Wrote pdb files with previous and current coordinates<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Step 21483, time 42.966 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.009368, max 0.641094 (between atoms 9 and 11)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
1 2 33.3 0.0928 0.0961 0.1000<br>
18 20 34.2 0.1474 0.1635 0.1470<br>
16 18 60.0 0.1842 0.1310 0.1330<br>
16 17 64.8 0.1447 0.1264 0.1230<br>
14 15 30.4 0.0979 0.1525 0.1530<br>
11 15 77.5 0.2435 0.1147 0.1470<br>
11 12 34.5 0.2609 0.1633 0.1470<br>
9 11 95.3 0.0397 0.2183 0.1330<br>
Wrote pdb files with previous and current coordinates<br>
... ... ...<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">log file at the start and just before the simulation blew up:<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><br>
Started mdrun on node 0 Wed Feb 15 14:46:26 2012<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> Step Time Lambda<br>
0 0.00000 0.00000<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Grid: 15 x 15 x 16 cells<br>
Energies (kJ/mol)<br>
Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih.<br>
3.62720e+04 5.42463e+03 1.35029e+04 1.73286e+04 3.49678e+03<br>
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)<br>
1.12718e+04 7.18682e+04 8.12244e+04 -7.18252e+03 -1.27427e+06<br>
Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En.<br>
-3.89615e+05 0.00000e+00 0.00000e+00 -1.43068e+06 2.42524e+05<br>
Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd<br>
-1.18815e+06 3.08494e+02 -1.97177e+02 5.79670e+02 1.01684e-05<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> Step Time Lambda<br>
500 1.00000 0.00000<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> Energies (kJ/mol)<br>
Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih.<br>
3.59484e+04 5.33007e+03 1.32268e+04 1.70061e+04 3.50560e+03<br>
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)<br>
1.10240e+04 7.14613e+04 8.03669e+04 -7.03778e+03 -1.26659e+06<br>
Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En.<br>
-3.88952e+05 5.48165e+01 9.39514e+00 -1.42466e+06 2.43342e+05<br>
Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd<br>
-1.18131e+06 3.09534e+02 -1.89310e+02 4.99800e+02 1.05856e-05<br>
<br>
... ...<br>
<br>
Step Time Lambda<br>
21000 42.00000 0.00000<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> Energies (kJ/mol)<br>
Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih.<br>
3.62118e+04 5.30282e+03 1.34838e+04 1.83737e+04 3.33814e+03<br>
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)<br>
1.12261e+04 6.97720e+04 8.28599e+04 -6.87470e+03 -1.25607e+06<br>
Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En.<br>
-3.87420e+05 4.27582e+01 6.98584e+00 -1.40975e+06 2.44245e+05<br>
Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd<br>
-1.16551e+06 3.10684e+02 -1.80638e+02 -5.00713e+02 1.04526e-05<o:p></o:p></span></p>
<p style="margin-bottom:12.0pt"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Large VCM(group Protein_POPC): 73.33204, 29.76558, -12.48454, Temp-cm: 2.95863e+05<br>
Large VCM(group Water_SOL_CL): -46.46529, -18.86033, 7.91055, Temp-cm: 3.35241e+04<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">iii) fc = 0<o:p></o:p></span></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">The end of the log file looks:<o:p></o:p></span></p>
<div id="divIP1">
<div id="divExp">
<div id="divBdy">
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> Step Time Lambda<br>
29000 58.00000 0.00000<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> Energies (kJ/mol)<br>
Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih.<br>
3.65061e+04 5.60824e+03 1.42205e+04 1.80483e+04 3.37686e+03<br>
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)<br>
1.09448e+04 6.89125e+04 8.18947e+04 -6.41177e+03 -1.21650e+06<br>
Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En.<br>
-3.85131e+05 0.00000e+00 4.54606e+05 -1.36853e+06 2.44457e+05<br>
Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd<br>
-1.12408e+06 3.10953e+02 -1.57129e+02 5.40099e+02 1.15690e-05<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> Step Time Lambda<br>
29500 59.00000 0.00000<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> Energies (kJ/mol)<br>
Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih.<br>
3.66857e+04 5.65841e+03 1.39441e+04 1.81639e+04 3.44242e+03<br>
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)<br>
1.11234e+04 6.94373e+04 8.36399e+04 -6.42711e+03 -1.21988e+06<br>
Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En.<br>
-3.85140e+05 0.00000e+00 4.73981e+05 -1.36935e+06 2.43700e+05<br>
Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd<br>
-1.12565e+06 3.09991e+02 -1.57883e+02 3.05347e+02 1.18083e-05<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><br>
-------------------------------------------------------<br>
Program mpich_exe.10603, VERSION 4.5.5<br>
Source code file: ns.c, line: 2549<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Fatal error:<br>
One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">The starting system has these dimensions 10.41535 10.32882 11.24541. Using g_energy to check the box size fluctuations, I got the following:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><br>
21<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Last energy frame read 297 time 59.400<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Statistics over 27501 steps [ 0.0000 through 55.0000 ps ], 1 data sets<br>
All statistics are over 2751 points<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Box-X 14.3931 1.2 2.47974 8.21254 (nm)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">22<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Last energy frame read 297 time 59.400<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Statistics over 27501 steps [ 0.0000 through 55.0000 ps ], 1 data sets<br>
All statistics are over 2751 points<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Box-Y 14.2735 1.2 2.45914 8.14431 (nm)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">23<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Last energy frame read 297 time 59.400<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Statistics over 27501 steps [ 0.0000 through 55.0000 ps ], 1 data sets<br>
All statistics are over 2751 points<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Box-Z 6.63204 1 2.01081 -6.84929 (nm)</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">The
<span style="color:black">graph</span>s<span style="color:#1F497D"> </span>of box sizes<span style="color:black"> show th</span>at x and y were increasing while z was decreasing drastically<span style="color:#1F497D">
</span>before the<span style="color:black"> </span>system blew up<span style="color:black">.</span><span style="color:#1F497D"><o:p></o:p></span></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Apologies for such a long post. I hope someone would have some clue as to why distance restraint can't be applied to my system. Your help is much
appreciated.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Best wishes,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Huiwen <o:p></o:p></span></p>
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