<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><BR><DIV><DIV>15 mar 2007 kl. 14.30 skrev sangeeta kundu:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV>Dear Tsjerk,</DIV> <DIV> My protein had -5.99 charge , so I added 6 NA+ atoms, not a single one.</DIV> <DIV> </DIV></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV>Nevertheless, 6 atoms is a very small tc-group. Large fluctuations in kinetic energy is expected for such a small collection of atoms, making the temperature coupling behave kind of wildly.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>/Erik</DIV><DIV><BR><BLOCKQUOTE type="cite"> <DIV>regards</DIV> <DIV>Sangeeta</DIV> <DIV><BR><BR><B><I>Tsjerk Wassenaar <<A href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</A>></I></B> wrote:</DIV> <BLOCKQUOTE class="replbq" style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Hi Sangeeta,<BR><BR>I think the problem is a lone sodium ion which is shaken vigorously<BR>round by its private heat bath, at some point getting too intimate<BR>with one of the water molecules around.<BR><BR>Never, never, NEVER give a handful of atoms, or a single atom, it's<BR>own heat bath! Put the sodium in with the solvent. Search the archives<BR>for tc-grps, temperature coupling, and such (and possibly my name), to<BR>get a fuller account. Besides that, you may be better off adding some<BR>additional sodium chloride... One sodium may balance the net charge,<BR>but it will not balance a charged protein.<BR><BR>Cheers,<BR><BR>Tsjerk<BR><BR><BR>On 3/15/07, sangeeta kundu wrote:<BR>> Dear All,<BR>><BR>> Thanks a lot to Mark,Tsjerk and Erik your promt reply.<BR>> It is a globular protein containing approximately 70<BR>> residues having crysal structure, without any<BR>> ligand,the simulation continued for 1.5 ns, & then<BR>> gave the segmentation fault, My .mdp file is given<BR>> below, I used SPC216 water and steepest descent for<BR>> minimisation, the emtol was 1000,it converged to that<BR>> within 800 steps.I used position restrained dynamics<BR>> for 50ps.The protein had -ve charge, so I added NA+<BR>> as counter ion.I used the same parameter<BR>> for carrying out the simualtion of the same protein at<BR>> 3/4 other tempeartures,the runs were completed without<BR>> giving any error.Waiting for your promt help.<BR>><BR>> title = Yo<BR>> cpp = /usr/bin/cpp<BR>> constraints = all-bonds<BR>> integrator = md<BR>> dt = 0.002 ; ps !<BR>> nsteps = 5000000 ; total 10 ns<BR>> nstcomm = 1<BR>> nstxout = 250<BR>> nstvout = 1000<BR>> nstfout = 0<BR>> nstlog = 100<BR>> nstenergy = 100<BR>> nstlist = 10<BR>> ns_type = grid<BR>> rlist = 1.0<BR>> rcoulomb = 1.0<BR>> rvdw = 1.0<BR>> ; Berendsen temperature coupling is on in two groups<BR>> Tcoupl = berendsen<BR>> tc-grps = Protein SOL NA+<BR>> tau_t = 0.1 0.1 0.1<BR>> ref_t = 523 523 523<BR>> ; Energy monitoring<BR>> energygrps = Protein SOL<BR>> ; Isotropic pressure coupling is now on<BR>> Pcoupl = berendsen<BR>> Pcoupltype = isotropic<BR>> tau_p = 0.5<BR>> compressibility = 4.5e-5<BR>> ref_p = 1.0<BR>> ; Generate velocites is off at 300 K.<BR>> gen_vel = no<BR>> gen_temp = 523.0<BR>> gen_seed = 173529<BR>><BR>><BR>><BR>> regards<BR>> Sangeeta<BR>> --- Tsjerk Wassenaar wrote:<BR>><BR>> > Hi Sangeeta,<BR>> ><BR>> > It would be helpful to us if you gave more<BR>> > information than "I tried<BR>> > to run a simulation and it crashed". What kind of<BR>> > protein, any<BR>> > ligands/non-standard groups. Did you perform energy<BR>> > minimization, etc,<BR>> > etc, etc... What's in the .mdp file?<BR>> ><BR>> > Tsjerk<BR>> ><BR>> > On 3/15/07, Erik Marklund <BR>> > wrote:<BR>> > ><BR>> > ><BR>> > > 15 mar 2007 kl. 08.29 skrev sangeeta kundu:<BR>> > ><BR>> > > Dear all,<BR>> > > I gave a simulation run of a protein using<BR>> > G43a1force field at 523K<BR>> > > using Berendson's Temperature coupling for 10<BR>> > ns, But three times it<BR>> > > failed with the messege "segmentation fault" ,<BR>> > without giving any other<BR>> > > error messege. Previously I ran the simualtion of<BR>> > the same protein at lower<BR>> > > temperature, (upto 473K) , and in all cases it ran<BR>> > successfully, but when I<BR>> > > used the temperature of 523 K it failed, I can not<BR>> > debug, please help.<BR>> > ><BR>> > ><BR>> > > I'm no expert, but I think a shorter timestep<BR>> > could be required for the<BR>> > > integrator to be stable when using such high<BR>> > temperatures, since the atoms<BR>> > > will move around quite fast.<BR>> > ><BR>> > ><BR>> > ><BR>> > > I have another question, Is there any way of<BR>> > analysing hydrogen bonds<BR>> > > on a residue basis? I mean to say how can I get<BR>> > the distribution of HBond<BR>> > > over residue number, I looked at g_hbond , but I<BR>> > could not get it.<BR>> > ><BR>> > ><BR>> > > It requires some postprocessing of the data, but<BR>> > the hbn- and hbm-output of<BR>> > > g_hbond together contains what you need to know<BR>> > about the hydrogen bonds on<BR>> > > an atom index basis. Now, you can easily go from<BR>> > the level of atoms to the<BR>> > > level of residues.<BR>> > ><BR>> > ><BR>> > ><BR>> > > regards<BR>> > > Sangeeta<BR>> > ><BR>> > > ________________________________<BR>> > > Here's a new way to find what you're looking for<BR>> > - Yahoo! Answers<BR>> > > _______________________________________________<BR>> > > gmx-users mailing list <A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> > > <A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>> > > Please don't post (un)subscribe requests to the<BR>> > list. Use the<BR>> > > www interface or send it to<BR>> > <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>> > > Can't post? Read<BR>> > > <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR>> > ><BR>> > > _______________________________________________<BR>> > > Erik Marklund, PhD student<BR>> > > Laboratory of Molecular Biophysics,<BR>> > > Dept. of Cell and Molecular Biology, Uppsala<BR>> > University.<BR>> > > Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>> > > phone: +46 18 471 4537 fax: +46 18 511 755<BR>> > > <A href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</A><BR>> > <A href="http://xray.bmc.uu.se/molbiophys">http://xray.bmc.uu.se/molbiophys</A><BR>> > ><BR>> > ><BR>> > > _______________________________________________<BR>> > > gmx-users mailing list <A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> > > <A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>> > > Please don't post (un)subscribe requests to the<BR>> > list. Use the<BR>> > > www interface or send it to<BR>> > <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>> > > Can't post? Read<BR>> > > <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR>> > ><BR>> ><BR>> ><BR>> > --<BR>> > Tsjerk A. Wassenaar, Ph.D.<BR>> > Junior UD (post-doc)<BR>> > Biomolecular NMR, Bijvoet Center<BR>> > Utrecht University<BR>> > Padualaan 8<BR>> > 3584 CH Utrecht<BR>> > The Netherlands<BR>> > P: +31-30-2539931<BR>> > F: +31-30-2537623<BR>> > _______________________________________________<BR>> > gmx-users mailing list <A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> > <A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>> > Please don't post (un)subscribe requests to the<BR>> > list. Use the<BR>> > www interface or send it to<BR>> > <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>> > Can't post? Read<BR>> > <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR>> ><BR>><BR>><BR>><BR>><BR>> __________________________________________________________<BR>> Yahoo! India Answers: Share what you know. Learn something new<BR>> <A href="http://in.answers.yahoo.com">http://in.answers.yahoo.com</A>/<BR>> _______________________________________________<BR>> gmx-users mailing list <A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> <A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>> Please don't post (un)subscribe requests to the list. Use the<BR>> www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>> Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR>><BR><BR><BR>-- <BR>Tsjerk A. Wassenaar, Ph.D.<BR>Junior UD (post-doc)<BR>Biomolecular NMR, Bijvoet Center<BR>Utrecht University<BR>Padualaan 8<BR>3584 CH Utrecht<BR>The Netherlands<BR>P: +31-30-2539931<BR>F: +31-30-2537623<BR>_______________________________________________<BR>gmx-users mailing list <A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><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? 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Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><BLOCKQUOTE type="cite"></BLOCKQUOTE><DIV>_______________________________________________</DIV><DIV>Erik Marklund, PhD student</DIV><DIV>Laboratory of Molecular Biophysics,</DIV><DIV>Dept. of Cell and Molecular Biology, Uppsala University.</DIV><DIV>Husargatan 3, Box 596,<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>75124 Uppsala, Sweden</DIV><DIV>phone:<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>+46 18 471 4537<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>fax: +46 18 511 755</DIV><DIV><A href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</A><SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>http://xray.bmc.uu.se/molbiophys</DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN> </DIV><BR></BODY></HTML>