<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Dear Justin</span></div><div><span>Hello :)</span></div><div><span>Thanks for your response. <br></span></div><div><span>You have mentioned that "</span>Position restraints are applied per [moleculetype], as indicated <br>in the topology". <br></div><div>In my topol.top file there are two .itp files included for the two protein chains. I opened the following file:</div>topol_Protein_chain_A.itp<br>Here I have :<br>---------------<br><div><span>[ moleculetype ]<br>; Name nrexcl<br>Protein_chain_A 3</span></div><div><span>---------------</span></div><div>1)))))) The molecultype has not mentioned explicitly protein as it is required by tc_grps (Protein non-Protein). <span style="color: rgb(0, 96, 191);">Does gromacs recognizes (Protein_chain_A)
as protein and so gives special thermostat to it????</span></div><div>=====================================</div><div>for the 1RFB protein having two chains, I did energy minimization and then NVT simulation for 200 ps and then used g_energy command to plot temperature.</div><div>using this command line:</div><div style="color: rgb(0, 96, 191);">g_energy -f nvt.mdp -o temp.xvg and then select 15 0 for temperature::::</div><div><br></div><div>Then it gives me temp.xvg output, but some warning are written on the screen. You can see them below:<br><span></span></div><div>------</div>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br><span style="color: rgb(0, 96,
191);">Temperature 309.834 0.17 3.51504 0.945045 (K)</span><br style="color: rgb(0, 96, 191);"><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191); font-weight: bold;">You may want to use the -driftcorr flag in order to correct</span><br style="color: rgb(0, 96, 191); font-weight: bold;"><span style="color: rgb(0, 96, 191); font-weight: bold;">for spurious drift in the graphs. Note that this is not</span><br style="color: rgb(0, 96, 191); font-weight: bold;"><span style="color: rgb(0, 96, 191); font-weight: bold;">a substitute for proper equilibration and sampling!</span><br><br>2----((what is the reason for spurious drist and is it necessary to be corrected?))<br style="color: rgb(0, 96, 191);"><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96,
191);">WARNING: nmol = 1, this may not be what you want.</span><br>(I do not understand this warning)<br style="color: rgb(0, 96, 191);"><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Temperature dependent fluctuation properties at T = 309.834.</span><br style="color: rgb(0, 96, 191);"><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Heat capacities obtained from fluctuations do *not* include</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">quantum corrections. If you want to get a more accurate estimate</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">please use the g_dos program.</span><br>3-----(It has mentioned that this program needs alot of memory. Is it really necessary to do this?)<br style="color: rgb(0, 96, 191);"><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">WARNING: Please verify that your simulations
are converged and perform</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">a block-averaging error analysis (not implemented in g_energy yet)</span><br><br>4------(What should I do for this warning)???<br style="color: rgb(0, 96, 191);"><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">========================================================<br><span style="color: rgb(0, 0, 0);">5----Although the two chains of my protein are identical, does it make trouble to have two separate .itp files for them? pdb2gmx with the option (chainsep) has given these two .itp files to me.</span><br style="color: rgb(0, 0, 0);"></span><br><div><br></div><div><br></div><div>Thanks alot for your valuable time....</div><div>Regards <br></div><div>Delara<br></div><div><br></div><div><br><span></span></div><div><br><span></span></div><div><span><br></span></div><div style="font-family: arial, helvetica, sans-serif;
font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b> delara aghaie <d_aghaie@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday, 16 June 2012, 15:37<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] simulating dimer proteins<br> </font> </div> <br><br><br>On 6/16/12 6:29 AM, delara aghaie wrote:<br>> Dear Mark<br>> Again some questions:<br>> ------------------------------------------<br>> I used -chainsep option to pdb2gmx and generated topology files for two protein<br>> chains and also .gro file containing both chains<br>>
........................................<br>> The energy minimization was done successfully and I got average pot.<br>> energy=-1.2*10^6<br>> Then I started NVT simulation for 200 ps with position restraints on proteins.<br>><br>> 1)) having the following line in .mdp file will do position restraints on both<br>> chains, considering that each chan has its own .top file????<br><br>Yes, it does. Position restraints are applied per [moleculetype], as indicated <br>in the topology.<br><br>> define = -DPOSRES ; position restrain the protein<br>> ---------------------------------<br>> 200 ps, NVT simulation finished, but I think there is something wrong here. This<br>> is part of my nvt.mdp file:<br>><br>> ; Temperature coupling is on<br>> tcoupl = V-rescale ; modified Berendsen thermostat<br>> tc-grps
= Protein Non-Protein ; two coupling groups - more accurate<br>> tau_t = 0.1 0.1 ; time constant, in ps<br>> ref_t = 310 310 ; reference temperature, one for each group, in K<br>><br>> As here my protein has two chains, is it necessary to increase the tc-groups???<br><br>No. See the following:<br><br><a href="http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do" target="_blank">http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do</a><br><br>-Justin<br><br>> I mean should I use for example<br>> tc-grps = Protein_chain_A Protein_chain_B SOl NA (These are the names that<br>> are present at the end of topol.top file)<br>><br>> Thanks<br>> Regards<br>> D.M<br>><br>><br>>
--------------------------------------------------------------------------------<br>><br>><br>><br>> --------------------------------------------------------------------------------<br>><br>><br>> *From:* Mark Abraham <<a ymailto="mailto:Mark.Abraham@anu.edu.au" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>> *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Saturday, 16 June 2012, 12:15<br>> *Subject:* Re: [gmx-users] simulating dimer proteins<br>><br>> On 16/06/2012 5:31 PM, delara aghaie wrote:<br>>> Dear Gromacs Users<br>>><br>>> Running pdb2gmx on a pdb file containing a dimer protein, I used option ((<br>>> chainsep id_or_ter)))<br>>> This resulted in separated topologies for each chain and separated posre<br>>> files. Also in the
.gro file, the aminoacides of the second chain started from<br>>> number 1. (Without this option the second chain aminoacides will receive<br>>> numbers in continuation of numbers of first chain))....<br>>><br>>> Now:<br>>> Can I use these files to continue the simulations or again it is necessary to<br>>> follow the procedure explained in multiple chains gromacs???<br>>><br>><br>> By definition of pdb2gmx function, you now have a topology and a coordinate file<br>> that matches. That is the minimum requirement for grompp to succeed later.<br>> grompp doesn't care about some aspects of atom numbering - including your<br>> observation above.<br>><br>> Mark<br>><br>> --<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a><br>> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>><br>><br>>
--<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a><br>> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>><br>><br>><br><br>-- <br>========================================<br><br>Justin A. Lemkul, Ph.D.<br>Research Scientist<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br><br><br><br><br> </div> </div> </div></body></html>