<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'bookman old style', 'new york', times, serif;font-size:12pt"><div><div style="font-family: arial, helvetica, sans-serif; font-size: 13px; ">Dear Mark....</div><div style="font-family: arial, helvetica, sans-serif; font-size: 13px; "><br>Thanks for your suggestions.</div><div style="font-family: arial, helvetica, sans-serif; font-size: 13px; ">1) Regarding to the g_sdf, the problem is I have 3 groups ( system, cation, anion) in my index file. </div><div style="font-family: arial, helvetica, sans-serif; font-size: 13px; "> But, before using g_sdf, I should have 4 groups. So, how about the last group?</div><div style="font-family: arial, helvetica, sans-serif; font-size: 13px; ">2) When I used g_sdf command ( g_sdf -s topol.tpr -f trj.trr -n index.ndx -r), it mention to select the group for 4 times. My question is, how
to select the group?</div><div style="font-family: arial, helvetica, sans-serif; font-size: 13px; "><br></div><div style="font-family: arial, helvetica, sans-serif; font-size: 13px; "><br></div><div style="font-family: arial, helvetica, sans-serif; font-size: 13px; ">THANKS</div><div style="font-family: arial, helvetica, sans-serif; font-size: 13px; "> IMA </div><div style="font-family: arial, helvetica, sans-serif; font-size: 13px; "><br></div></div><div style="font-family:bookman old style, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> "gmx-users-request@gromacs.org" <gmx-users-request@gromacs.org><br><b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org<br><b><span style="font-weight: bold;">Sent:</span></b> Wed, October 21, 2009 3:22:12 PM<br><b><span
style="font-weight: bold;">Subject:</span></b> gmx-users Digest, Vol 66, Issue 135<br></font><br>
Send gmx-users mailing list submissions to<br> <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br><span> <a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br>or, via email, send a message with subject or body 'help' to<br> <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br><br>You can reach the person managing the list at<br> <a ymailto="mailto:gmx-users-owner@gromacs.org" href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br><br><br>Today's
Topics:<br><br> 1. Re: Re: Chloroform (CHCl3) solvent box for G53a5 force field<br> (Justin A. Lemkul)<br> 2. why are the values of the LJ interaction energy negative and<br> the values of the Coulomb interaction energy positive between two<br> group. (Jinyao Wang)<br> 3. Re: why are the values of the LJ interaction energy negative<br> and the values of the Coulomb interaction energy positive between<br> two group. (Mark Abraham)<br> 4. Fatal error: 2 particles communicated to PME node 0 are more<br> than a cell length out of the domain decomposition cell of their<br> charge group (wuxiao)<br> 5. Re: Fatal error: 2 particles communicated to PME
node 0 are<br> more than a cell length out of the domain decomposition cell of<br> their charge group (Mark Abraham)<br> 6. g_rdf and number of atoms to include (Enemark Soeren)<br> 7. how to calculate g_sdf and ionic conductivity<br> (naimah haron naimah)<br> 8. Re: how to calculate g_sdf and ionic conductivity (Mark Abraham)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Tue, 20 Oct 2009 19:18:05 -0400<br>From: "Justin A. Lemkul" <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>Subject: Re: [gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5<br> force field<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>Message-ID: <<a ymailto="mailto:4ADE452D.6090602@vt.edu" href="mailto:4ADE452D.6090602@vt.edu">4ADE452D.6090602@vt.edu</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br><br><br>Pablo Englebienne wrote:<br><br>> Thanks for confirming this, Justin.<br>> <br>> I decided not to use the user-contributed CHCl3 box because the topology <br>> is not consistent with the GROMOS atom types: the CH is united atom <br>> (although the mass is 12.01100, it should probably be 13.01900?), while <br>> in G53a5 there are parameters for C, H and Cl. Has someone ever used <br>> this box successfully?<br>> <br>> I was able to equilibrate the box in NVT (100-200ps gives a stable <br>> simulation), although it exploded at constant pressure. After looking at <br>> some references on the mailing lists (both GMX and AMBER), I tried <br>>
increasing tau_p from 2.0 to 5.0 and that yielded a stable 100 ps <br>> simulation, although the system later (continuing for further ~150 ps) <br>> started to oscillate wildly in temperature and pressure.<br>> <br>> What is the effect of increasing tau_p? Besides making the dynamics <br>> stable, would changing its value affect the outcome of the simulation in <br>> any other way?<br><br>By increasing tau_p you are reducing the stringency of the pressure coupling, <br>i.e. allowing the system to change a bit more between coordinate scaling. By <br>decreasing the frequency of coordinate scaling in extremis, you would lose the <br>benefit of pressure coupling and achieve an NVT ensemble, with the box <br>dimensions being essentially static. In the case of a tau_p of 2.0 vs. 5.0, you <br>should not have this problem.<br><br>If the provided box uses a united-atom CH, I would suspect it is not suitable <br>for GROMOS96
parameters, as you have discovered. In all G96 variants, the H is <br>explicitly represented. You might consider coming up with your own box. Start <br>with a coordinate file for one molecule, use genconf to generate a box, and <br>equilibrate.<br><br>If you want any further information about diagnosing the current problem, <br>posting the .mdp file would be helpful.<br><br>-Justin<br><br>> <br>> Thanks again!<br>> _______________________________________________<br>> gmx-users mailing list <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><span>> Please search the archive at <a target="_blank" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!</span><br>> Please don't post
(un)subscribe requests to the list. Use thewww <br>> 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><span>> Can't post? Read <a target="_blank" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></span><br>> <br><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br><span><a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br><br>========================================<br><br><br>------------------------------<br><br>Message: 2<br>Date: Wed, 21 Oct 2009 10:18:19
+0800<br>From: "Jinyao Wang" <<a ymailto="mailto:wangjy@ciac.jl.cn" href="mailto:wangjy@ciac.jl.cn">wangjy@ciac.jl.cn</a>><br>Subject: [gmx-users] why are the values of the LJ interaction energy<br> negative and the values of the Coulomb interaction energy positive<br> between two group.<br>To: "gmx-users" <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a ymailto="mailto:456090806.02727@ciac.jl.cn" href="mailto:456090806.02727@ciac.jl.cn">456090806.02727@ciac.jl.cn</a>><br>Content-Type: text/plain; charset="gb2312"<br><br>Hi gmx-users,<br> I have calculated the interaction energy between two group. But I find that the values of the LJ interaction energy are negative and the values of the Coulomb interaction energy are positive between two group. So I think the LJ interaction is
attractive and the Coulomb interaction is repulsive. Is it correct for my consideration of the interaction ? <br> <br><br> <br> <br><br> Jinyao Wang<br> <a ymailto="mailto:wangjy@ciac.jl.cn" href="mailto:wangjy@ciac.jl.cn">wangjy@ciac.jl.cn</a><br> 2009-10-21<br><br>------------------------------<br><br>Message: 3<br>Date: Wed, 21 Oct 2009 13:26:22 +1100<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>Subject: Re: [gmx-users] why are the values of the LJ interaction<br> energy negative and the values of the Coulomb interaction energy<br> positive between two group.<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>Message-ID: <<a ymailto="mailto:4ADE714E.5000704@anu.edu.au" href="mailto:4ADE714E.5000704@anu.edu.au">4ADE714E.5000704@anu.edu.au</a>><br>Content-Type: text/plain; charset=GB2312<br><br>Jinyao Wang wrote:<br>> Hi gmx-users,<br>> I have calculated the interaction energy between two group. But I find that the values of the LJ interaction energy are negative and the values of the Coulomb interaction energy are positive between two group. So I think the LJ interaction is attractive and the Coulomb interaction is repulsive. Is it correct for my consideration of the interaction ? <br><br>Maybe. That conclusion would assume<br>a) that you've calculated it correctly,<br>b) that the model physics is robust with respect to such a decomposition<br>when it almost certainly wasn't
parameterized for such a property, and<br>c) the decomposed interaction energy means anything.<br><br>Mark<br><br><br>------------------------------<br><br>Message: 4<br>Date: Wed, 21 Oct 2009 10:31:49 +0800<br>From: wuxiao <<a ymailto="mailto:xiaowu759@hotmail.com" href="mailto:xiaowu759@hotmail.com">xiaowu759@hotmail.com</a>><br>Subject: [gmx-users] Fatal error: 2 particles communicated to PME node<br> 0 are more than a cell length out of the domain decomposition cell of<br> their charge group<br>To: <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a ymailto="mailto:BAY131-W17839D5AC63D6A98F4E4ECE9BF0@phx.gbl" href="mailto:BAY131-W17839D5AC63D6A98F4E4ECE9BF0@phx.gbl">BAY131-W17839D5AC63D6A98F4E4ECE9BF0@phx.gbl</a>><br>Content-Type: text/plain; charset="gb2312"<br><br><br>Dear GMXers,<br><br> When I perfomed a MD
simulation, it always teminated after about 700 ps with the message:<br><br>Fatal error: 2 particles communicated to PME node 0 are more than a cell length out of the domain decomposition cell of their charge group<br><br> I utilized the GROMACS-4.0.5. I have searched the maillist to find some similar posts but they can not yet cope with this issues. Could you give me some clues, please?<br><br> Best wishes,<br><br> Chaofu Wu, Dr.<br> <br>_________________________________________________________________<br>Messenger安全保护中心，免费修复系统漏洞，保护Messenger安全！<br><span><a target="_blank" href="http://im.live.cn/safe/">http://im.live.cn/safe/</a></span><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br><span>URL: <a target="_blank"
href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20091021/c8985b2e/attachment-0001.html">http://lists.gromacs.org/pipermail/gmx-users/attachments/20091021/c8985b2e/attachment-0001.html</a></span><br><br>------------------------------<br><br>Message: 5<br>Date: Wed, 21 Oct 2009 13:58:24 +1100<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>Subject: Re: [gmx-users] Fatal error: 2 particles communicated to PME<br> node 0 are more than a cell length out of the domain decomposition<br> cell of their charge group<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>Message-ID: <<a ymailto="mailto:4ADE78D0.2000304@anu.edu.au"
href="mailto:4ADE78D0.2000304@anu.edu.au">4ADE78D0.2000304@anu.edu.au</a>><br>Content-Type: text/plain; charset=GB2312<br><br>wuxiao wrote:<br>> Dear GMXers,<br>> When I perfomed a MD simulation, it always teminated after about 700 <br>> ps with the message:<br>> /Fatal error: 2 particles communicated to PME node 0 are more than a <br>> cell length out of the domain decomposition cell of their charge group/<br>> I utilized the GROMACS-4.0.5. I have searched the maillist to find <br>> some similar posts but they can not yet cope with this issues. Could you <br>> give me some clues, please?<br><br><span>Yep. <a target="_blank" href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a></span><br><br>Mark<br><br><br>------------------------------<br><br>Message: 6<br>Date: Wed, 21 Oct 2009 13:28:39 +0800<br>From: "Enemark Soeren"
<<a ymailto="mailto:chees@nus.edu.sg" href="mailto:chees@nus.edu.sg">chees@nus.edu.sg</a>><br>Subject: [gmx-users] g_rdf and number of atoms to include<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>Message-ID:<br> <<a ymailto="mailto:C178399C57FF284FA0022B75E348721905E7A9BF@MBX03.stf.nus.edu.sg" href="mailto:C178399C57FF284FA0022B75E348721905E7A9BF@MBX03.stf.nus.edu.sg">C178399C57FF284FA0022B75E348721905E7A9BF@MBX03.stf.nus.edu.sg</a>><br>Content-Type: text/plain; charset="us-ascii"<br><br>Dear users,<br><br> <br><br>I would like to compare interactions between molecules by using RDF. I<br>have tried looking at glycine and water, and compare the following two<br>interactions:<br><br>1) between the amine hydrogen atoms in glycine and the oxygen atom<br>in water<br><br>2)
between the carboxyl oxygen atoms in glycine and the oxygen atom<br>in water<br><br> <br><br>However, my result in 1) depends on how many of the 3 hydrogen atoms I<br>include in the calculations. Why is that? Does that mean that I cannot<br>directly compare the strengths (RDF peak height) of the two interactions<br>as they are not based on the same number of atoms? Does it also mean<br>that I must always calculate RDFs by using 1 atom on each of the<br>particles/groups that I am comparing?<br><br> <br><br>Thanks,<br><br>Soren<br><br> <br><br> <br><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br><span>URL: <a target="_blank" href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20091021/31a92441/attachment-0001.html">http://lists.gromacs.org/pipermail/gmx-users/attachments/20091021/31a92441/attachment-0001.html</a></span><br><br>------------------------------<br><br>Message: 7<br>Date: Tue, 20 Oct 2009
23:48:12 -0700 (PDT)<br>From: naimah haron naimah <<a ymailto="mailto:cimot_ima98@yahoo.com" href="mailto:cimot_ima98@yahoo.com">cimot_ima98@yahoo.com</a>><br>Subject: [gmx-users] how to calculate g_sdf and ionic conductivity<br>To: gromacs <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a ymailto="mailto:662629.64091.qm@web36505.mail.mud.yahoo.com" href="mailto:662629.64091.qm@web36505.mail.mud.yahoo.com">662629.64091.qm@web36505.mail.mud.yahoo.com</a>><br>Content-Type: text/plain; charset="us-ascii"<br><br>Hello all........<br><br>Did anyone know how to <br>1) calculate g_sdf? <br>2) ionic conductivity? <br><br>Can I have the commands for that.... <br><br>Thanks<br><br>IMA<br><br><br><br> <br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br><span>URL: <a target="_blank"
href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20091020/7469faa9/attachment-0001.html">http://lists.gromacs.org/pipermail/gmx-users/attachments/20091020/7469faa9/attachment-0001.html</a></span><br><br>------------------------------<br><br>Message: 8<br>Date: Wed, 21 Oct 2009 18:20:40 +1100<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>Subject: Re: [gmx-users] how to calculate g_sdf and ionic conductivity<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>Message-ID: <<a ymailto="mailto:4ADEB648.1010308@anu.edu.au" href="mailto:4ADEB648.1010308@anu.edu.au">4ADEB648.1010308@anu.edu.au</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>naimah haron naimah wrote:<br>> Hello all........<br>> <br>> Did
anyone know how to<br>> 1) calculate g_sdf?<br><br>Start with g_sdf -h.<br><br>> 2) ionic conductivity?<br><br>Don't know. Look in manual 7.4, 8 and maybe Appendix D.<br><br>> Can I have the commands for that....<br><br>If you do some more of your own work and ask focussed questions you help <br>yourself look worth helping :-)<br><br>Mark<br><br><br>------------------------------<br>Dear Mark....</div><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><br>Thanks for your suggestions.</div><div style="font-family:arial, helvetica, sans-serif;font-size:13px">1) Regarding to the g_sdf, the problem is I have 3 groups ( system, cation, anion) in my index file. </div><div style="font-family:arial, helvetica, sans-serif;font-size:13px"> But, before using g_sdf, I should have 4 groups. So, how about the last group?</div><div style="font-family:arial, helvetica, sans-serif;font-size:13px">2) When I used
g_sdf command ( g_sdf -s topol.tpr -f trj.trr -n index.ndx -r), it mention to select the group for 4 times. My question is, how to select the group?</div><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><br></div><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><br></div><div style="font-family:arial, helvetica, sans-serif;font-size:13px">THANKS</div><div style="font-family:arial, helvetica, sans-serif;font-size:13px"> IMA </div><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><br></div><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><br></div><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><br></div><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><br></div><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><br></div><div style="font-family:arial, helvetica,
sans-serif;font-size:13px">_____________________________________________<br>gmx-users mailing list<br><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/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br><br>End of gmx-users Digest, Vol 66, Issue 135<br>******************************************<br></div></div><div style="position:fixed"></div></div><br>
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