<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV>I'd say the mdp looks fine, after a quick glace at it.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Didn't pdb2gmx give you information about the charge state of the protein? There is a bunch of papers out there assessing the importance of ions in simulations of both neutral and charged solutes. It will depend on your protein and the scientific question you intend to investigate.</DIV><DIV><BR class="khtml-block-placeholder"></DIV>As Mark mentioned, a general answer to wether the a simulation is "correct" is hard to give. I suggest to have a look at the energies, temperatures and structures from the simulation to begin with. It might give away flaws in the system preparation or simulation parameters.<DIV><BR class="khtml-block-placeholder"></DIV><DIV>/Erik<DIV><BR><DIV><DIV>7 feb 2007 kl. 13.24 skrev sangeeta kundu:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV>Dear Sir,</DIV> <DIV> </DIV> <DIV> Thanks for your prompt reply, It seems that we do not have to bother about whether the protein is coming out of the box or not as already we introduced pbc? Then how should we understand that the simulation is correct?</DIV> <DIV> Will you please kindly check over my md.mdp file, Another trouble I was facing that when running grompp it did not give any information about charge, previously when I ran the same for other proteins it always gave information about charge, so I had to add counter ion , but here I did not. Am I doing any mistake?</DIV> <DIV> Please help.</DIV> <DIV> </DIV> <DIV>regards</DIV> <DIV>SANGEETA</DIV> <DIV><BR><BR><B><I>Erik Marklund <<A href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</A>></I></B> wrote:</DIV> <BLOCKQUOTE class="replbq" style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"><BR> <DIV> <DIV>7 feb 2007 kl. 12.48 skrev sangeeta kundu:</DIV><BR class="Apple-interchange-newline"> <BLOCKQUOTE type="cite"> <DIV><STRONG><FONT face="times new roman" size="3">Dear Sir,</FONT></STRONG></DIV> <DIV><STRONG><FONT face="Times New Roman" size="3"></FONT></STRONG> </DIV> <DIV><STRONG><FONT face="times new roman" size="3"> I am facing one problem, I gave the MD run of a protein of approximately 70 residues for 10ns, after 1 ns run part of protein was getting out of the waterbox and at the end of 10 ns I found that almost half of the protein was coming out of the waterbox, I gave the simulation under NPT condition at 46C and 1BAR pressure, I used 43a1 force field and spc water.</FONT></STRONG></DIV></BLOCKQUOTE> <DIV><BR class="khtml-block-placeholder"></DIV> <DIV>Why would this be a problem? Proteins do diffuse you know. And since you have pbc the protein cannot really leave the waterbox.</DIV> <DIV><BR class="khtml-block-placeholder"></DIV> <DIV>/Erik</DIV><BR> <BLOCKQUOTE type="cite"> <DIV> </DIV> <DIV><STRONG><FONT face="Times New Roman" size="3">This is my md.mdp file</FONT></STRONG></DIV> <DIV><STRONG><FONT face="Times New Roman"></FONT></STRONG> </DIV> <DIV><STRONG><FONT face="Times New Roman"> <FONT color="#7f007f" size="3">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>pbc = xyz<BR>coulombtype = PME<BR>rlist = 0.9<BR>rcoulomb = 0.9<BR>rvdw = 0.9<BR>fourierspacing = 0.12<BR>pme_order = 4<BR>ewald_rtol = 1e-5<BR>; Berendsen temperature coupling is on in two groups<BR>Tcoupl = berendsen<BR>tc-grps = Protein SOL<BR>tau_t = 0.1 0.1<BR>ref_t = 319 319<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 = 319.0<BR>gen_seed = 173529<BR></FONT></FONT></STRONG></DIV> <DIV><STRONG><FONT face="Times New Roman" size="3">I used the 43a1 force field, and prepared the water box by the commands </FONT></STRONG></DIV> <DIV><STRONG><FONT face="Times New Roman" color="#007f40" size="3">editconf -bt triclinic -f conf.pdb -o box.pdb -c -d 1.0 </FONT></STRONG></DIV> <DIV><STRONG><FONT face="Times New Roman" color="#007f40" size="3">genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top</FONT></STRONG></DIV> <DIV><STRONG><FONT face="Times New Roman" color="#007f40" size="3"></FONT></STRONG> </DIV> <DIV><STRONG><FONT face="Times New Roman" color="#007f40" size="3"><FONT color="#000000">But I wonder that</FONT> </FONT><FONT face="times new roman"> <FONT size="3">while executing the command</FONT></FONT></STRONG><FONT size="3"> </FONT></DIV> <DIV><FONT color="#007f40"><FONT size="3"><STRONG><FONT face="times new roman">grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr</FONT></STRONG> </FONT></FONT></DIV> <DIV><FONT color="#007f40" size="3"></FONT> </DIV> <DIV><FONT color="#007f40"><FONT size="3"><FONT face="times new roman" color="#000000"><STRONG>it did not display any charge , so I did not add any counterion to my protein, in the subsequent steps em.pdb and pr.mdp files were produced and in both the cases the protein was almost in the centre of the box, while I took the snapshot after 1ns the protein was still at the centre , but after 1 ns it was coming to one corner of the box, and finally almost half of it was outside the box when I completed the run, I can not detect why it is coming outside the box?</STRONG></FONT></FONT></FONT></DIV> <DIV> </DIV> <DIV><FONT color="#007f40"><FONT size="3"><FONT face="times new roman" color="#000000"><STRONG>Where am I doing mistake? Another question is how can I understand that the simulation has been completed successfully?</STRONG></FONT></FONT></FONT></DIV> <DIV><FONT color="#007f40"><FONT size="3"><FONT face="times new roman" color="#000000"><STRONG>Please help.</STRONG></FONT></FONT></FONT></DIV> <DIV><FONT color="#007f40"><FONT size="3"><FONT face="times new roman" color="#000000"><STRONG>regards</STRONG></FONT></FONT></FONT></DIV> <DIV><FONT color="#007f40"><FONT size="3"><FONT face="times new roman" color="#000000"><STRONG>SANGEETA </STRONG></FONT></FONT></FONT></DIV> <DIV><STRONG><FONT face="Times New Roman" color="#007f7f" size="3"></FONT></STRONG> </DIV> <DIV><STRONG><FONT face="Times New Roman" size="3"></FONT></STRONG> </DIV> <DIV><STRONG><FONT face="Times New Roman" size="3"></FONT></STRONG> </DIV> <DIV> </DIV> <DIV><BR class="khtml-block-placeholder"></DIV> <HR size="1"> Here’s a new way to find what you're looking for - <A href="http://us.rd.yahoo.com/mail/in/yanswers/*http://in.answers.yahoo.com/">Yahoo! Answers</A> <DIV style="MARGIN: 0px">_______________________________________________</DIV> <DIV style="MARGIN: 0px">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV> <DIV style="MARGIN: 0px"><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV> <DIV style="MARGIN: 0px">Please don't post (un)subscribe requests to the list. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV> <DIV style="MARGIN: 0px">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV> <DIV style="MARGIN: 0px">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></DIV></DIV></BODY></HTML>