<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>Hi,</div><div><br></div><div>the rmsd you show is for the protein in vacuum? It goes up to 0.7 nm! That is a very</div><div>large deformation, is it expected? Isn't your protein freezing and all the kinetic energy</div><div>going into translational motion.</div><div><br></div><div>there is a few things you could try. </div><div>1- First you should increase the rlilst to at least 1.3 but 1.4 would be better. </div><div>2- And/or reduce the nstlist to 5. </div><div><br></div><div>You should modify at least one of the two, that will increases the cost of your simulation </div><div>but should make increase energy conservation.</div><div><br></div><div>Then you should try a smaller time step 0.020 ps might just remove all the lincs warnings.</div><div><br></div><div>XAvier.</div><div><br><blockquote type="cite"><font class="Apple-style-span" color="#000000"><br></font><br><div class="gmail_quote">On Fri, Apr 16, 2010 at 5:17 PM, Martti Louhivuori <span dir="ltr"><<a href="mailto:m.j.louhivuori@rug.nl" target="_blank">m.j.louhivuori@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <div>On 15 Apr 2010, at 18:06, Trang wrote:<br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> My target system is a protein with lipid molecules added randomly (using GENBOX). Running MD, I expect to<br> </blockquote> <br></div> I hope you're using a larger van der Waals distance (0.24nm or so) when inserting the lipids.</blockquote><div> </div><div>I tried 0.3 - 0.5. It looked fine, but didn't work. <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <div><br> <br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> broke down the problem, that is, to run md simulation for the protein molecule only, and in vacuum. Still no improvement. Although all the distances in the minimized structure are visually proper, the system exploded.<br> </blockquote> <br></div> If you can't run the protein even in vacuum, then the problem is either in your MD parameters, starting co-ordinates or some simple mistake somewhere. Since the .mdp files you posted seem ok, my bet is on the starting co-ordinates, just as Xavier proposed.<br> <br></blockquote><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Could you post the system topology (.top) and the protein topology (.itp), so we can rule out any mistakes in those?</blockquote><div><br>The protein topo is too large, so I put it here. <a href="http://pastie.org/926617">http://pastie.org/926617</a><br> Here is the system topology.<br><br>----------------------------<br>#include "../martini_v2.1.itp"<br>#include "../martini_v2.1_aminoacids.itp"<br>#include "11BHSD1.itp"<br><br>; Include Position restraint file<br> #ifdef POSRES<br>#include "posre.itp"<br>#endif<br><br><br>[ system ]<br>11BHSD1 <br><br>[ molecules ]<br>11BHSD1 1<br>----------------------------<br><br> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> You should also double check whether you have close contacts between some atoms in the protein; e.g. in VMD this is easily done using the "dynamic bonds" representation. </blockquote><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <br> -martti-<br></blockquote><br>Minimized structure showed no close contact (with distance cutoff 1.6, even to 1.9). Production run stopped at step 175552 (5266.56 ps) with Segmentation fault, preceeded with a lot of Lincs warnings (I set ring_bonds = "constraints"). This is the mdp file, this file goes along with the system in vaccuum that crashed. I'm not sure if too long simulation time can be the cause. The strange thing is that the system seemed to be relatively stable at the time of crash. rmds.xvg is below, in case you want to see the graph first-hand.<br> <br>-------------------------MD---------------------------<br>integrator = md<br>tinit = 0.0<br>dt = 0.030<br>nsteps = 900000<br>nstcomm = 1<br> comm-grps =<br>nstxout = 5000<br>nstvout = 5000<br>nstfout = 0<br>nstlog = 2000<br>nstenergy = 2000<br>nstxtcout = 1000<br> xtc_precision = 100<br>xtc-grps =<br>energygrps =<br>nstlist = 10<br>ns_type = grid<br>pbc = xyz<br>rlist = 1.2<br> coulombtype = Shift<br>rcoulomb_switch = 0.0<br>rcoulomb = 1.2<br>epsilon_r = 15<br>vdw_type = Shift<br>rvdw_switch = 0.9<br>rvdw = 1.2<br> DispCorr = No<br>tcoupl = Berendsen<br>tc-grps = Protein<br>tau_t = 0.3<br>ref_t = 323<br>Pcoupl = berendsen<br>Pcoupltype = isotropic<br> tau_p = 3.0<br>compressibility = 3e-5<br>ref_p = 1.0<br>gen_vel = no<br>gen_temp = 323<br>gen_seed = 666<br>constraints = none<br> constraint_algorithm = Lincs<br>unconstrained_start = no<br>lincs_order = 4<br>lincs_warnangle = 30<br>----------------------------------------------------------<br><br>-------------rmsd.xvg-------------------------------<br> @ title "RMSD"<br>@ xaxis label "Time (ps)"<br>@ yaxis label "RMSD (nm)"<br>@TYPE xy<br>@ subtitle "Protein after lsq fit to Protein"<br> 0.0000000 0.0001400<br> 150.0000000 0.6150032<br> 300.0000000 0.6162945<br> 450.0000000 0.6451609<br> 600.0000000 0.6317724 <br> 750.0000000 0.6501579<br> 900.0000000 0.6642945<br>1050.0000000 0.6742513<br>1200.0000000 0.6651280<br>1350.0000000 0.6965100<br> 1500.0000000 0.6856629<br>1650.0000000 0.7271055<br>1800.0000000 0.7174531<br>1950.0000000 0.7088170<br>2100.0000000 0.7492073<br>2250.0000000 0.7352809<br>2400.0000000 0.7196461<br>2550.0000000 0.7162255<br> 2700.0000000 0.7277457<br>2850.0000000 0.7121301<br>3000.0000000 0.7084662<br>3150.0000000 0.7153199<br>3300.0000000 0.7209989<br>3450.0000000 0.7342823<br>3600.0000000 0.7297466<br>3750.0000000 0.7254455<br> 3900.0000000 0.7175814<br>4050.0000000 0.7134616<br>4200.0000000 0.7212958<br>4350.0000000 0.7258847<br>4500.0000000 0.7201833<br>4650.0000000 0.7286560<br>4800.0000000 0.7188574<br>4950.0000000 0.7177775<br> 5100.0000000 0.7247230<br>5250.0000000 0.7153631<br>-----------------------------------------------------------<br><br><br></div> -- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br></body></html>