<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><BR>Dear Justin,</DIV>
<DIV> <SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Nimbus Roman No9 L','serif'; mso-bidi-font-size: 12.0pt; mso-fareast-font-family: 'Nimbus Sans L'; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: #00FF; mso-bidi-language: AR-SA">i am trying to insert a peptide in trans-bialyer orientation into a </SPAN><SPAN style="FONT-SIZE: 12pt; FONT-FAMILY: 'Nimbus Roman No9 L','serif'; mso-fareast-font-family: 'Nimbus Sans L'; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: #00FF; mso-bidi-language: AR-SA">pre-equilibrated POPC bilayer using <A href="http://moose.bio.ucalgary.ca/files/inflategro"><B style="mso-bidi-font-weight: normal"><FONT color=#000080>inflategro</FONT></B></A> script. After 13 steps of compression, the area per lipid is 2.61956768363491 nm^2, whereas the desired
area per lipid is 0.658 nm^2. But when i try to energy minimize the compressed structure after 13th steps of compression, the energy did not converged and give the following errors. During em i use strong position restraints on peptide heavy atom using force constants of 100000.<BR>------------------------------<BR>perl inflategro em_13.gro 0.95 POPC 0 com_13.gro 5 area_lip.dat <BR>grompp -f enermin.mdp -c com_13.gro -p system.top -o em_14.tpr<BR>mdrun -s em_14.tpr -nice 4 -o em_14 -c em_14 -e em_14 -g em_14&<BR>Reading file em_14.tpr, VERSION 3.3.1 (single precision)<BR>Steepest Descents:<BR> Tolerance (Fmax) = 1.00000e+03<BR> Number of steps = 50000<BR><BR>Step 9, time 0.018 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 0.001381 (between atoms 72 and 74) rms 0.000054<BR>bonds that rotated more than 30
degrees:<BR> atom 1 atom 2 angle previous, current, constraint length<BR> 539 540 35.7 0.1000 0.1000 0.1000<BR><BR>Step 15, time 0.03 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 0.003842 (between atoms 65 and 68) rms 0.000141<BR>bonds that rotated more than 30 degrees:<BR> atom 1 atom 2 angle previous, current, constraint length<BR> 539 540 38.3 0.1000 0.1000 0.1000<BR><BR>Step 16, time 0.032 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 0.016511 (between atoms 65 and 68) rms 0.000550<BR>bonds that rotated more than 30 degrees:<BR> atom 1 atom 2 angle previous, current, constraint length<BR>
65 66 42.8 0.1390 0.1412 0.1390<BR> 65 68 42.9 0.1390 0.1413 0.1390<BR> 66 70 41.9 0.1390 0.1411 0.1390<BR> 68 72 41.1 0.1390 0.1411 0.1390<BR> 70 74 39.6 0.1390 0.1407 0.1390<BR> 72 74 38.7 0.1390 0.1406 0.1390<BR> 344 345
34.8 0.1390 0.1397 0.1390<BR> 344 347 34.4 0.1390 0.1397 0.1390<BR> 345 349 33.6 0.1390 0.1397 0.1390<BR> 347 351 33.1 0.1390 0.1397 0.1390<BR> 349 353 32.7 0.1390 0.1397 0.1390<BR> 351 353 32.6 0.1390 0.1397 0.1390<BR> 381 382 33.3 0.1390 0.1396
0.1390<BR> 381 384 33.5 0.1390 0.1396 0.1390<BR> 382 386 32.9 0.1390 0.1396 0.1390<BR> 384 388 33.2 0.1390 0.1396 0.1390<BR> 386 390 32.4 0.1390 0.1396 0.1390<BR> 388 390 32.5 0.1390 0.1396 0.1390<BR> 539 540 49.3 0.1000 0.1000 0.1000<BR> 546 547 33.5
0.1250 0.1250 0.1250<BR><BR>Stepsize too small, or no change in energy.<BR>Converged to machine precision,<BR>but not to the requested precision Fmax < 1000<BR><BR><B style="mso-bidi-font-weight: normal">Double precision normally gives you higher accuracy.</B><BR><B style="mso-bidi-font-weight: normal">You might need to increase your constraint accuracy, or turn</B><BR><B style="mso-bidi-font-weight: normal">off constraints alltogether (set constraints = none in mdp file)</B><BR><BR>writing lowest energy coordinates.<BR><BR>Steepest Descents converged to machine precision in 43 steps,<BR>but did not reach the requested Fmax < 1000.<BR>Potential Energy = -1.2865473e+05<BR>Maximum force = 4.7082656e+04 on atom 547<BR>Norm of force = 6.7057188e+04<BR><BR>gcq#38: "I'm Your Worst Nightmare"
(Creep)<BR><BR>-------------------------------------------------------------------------<BR>my enermin.mdp file is .......................<BR>-------------------------------------------------<BR>title = sp position restraining<BR>cpp = /usr/bin/cpp<BR>define = -DPOSRES<BR>constraints = all-bonds<BR>constraint_algorithm= lincs<BR>lincs_order = 4<BR>lincs_iter = 6<BR>lincs_warnangle = 30<BR>integrator =
steep ; Algorithm (steep = steepest descent minimization)<BR>dt = 0.002 ; ps !<BR>nsteps = 50000 ; Maximum number of (minimization) steps to perform<BR>nstlog = 200<BR>nstlist = 1<BR>ns_type = grid<BR>rlist = 1.2 ; Cut-off for making neighbor list (short range
forces)<BR>rcoulomb = 1.2<BR>rvdw = 1.2<BR>coulombtype = PME<BR>fourierspacing = 0.12<BR>fourier_nx = 0<BR>fourier_ny = 0<BR>fourier_nz = 0<BR>pme_order = 4<BR>ewald_rtol = 1e-5<BR>optimize_fft = yes<BR>pbc = xyz ; Periodic Boundary
Conditions (yes/no)<BR>;<BR>; Energy minimizing stuff<BR>;<BR>emtol = 1000<BR>emstep = 0.01<BR> <BR><BR>---------------<BR>should i continue further compression with this energy minimized structure (em_14.gro)??<BR>if not how can i slove this problem.<BR>waiting for ur suggestion.<BR>Moutusi Manna<BR style="mso-special-character: line-break"><BR style="mso-special-character: line-break"></SPAN></DIV>
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