Hi, <br><br>In the file FF.dat, it is mentioned that GROMACS force fields ffgmx and ffgmx2 are DEPRECATED in the brackets. Does it mean I should not use it?<br><br>Can someone help me with this?<br><br>Mohan <br><br><div><span class="gmail_quote">
On 27/04/06, <b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:
</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Send gmx-users mailing list submissions to<br> <a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>or, via email, send a message with subject or body 'help' to
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</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. Change default "nice" option for mdrun (was: Can not find
<br> file: topol.tpr) (Guillem Plasencia)<br> 2. RE: Coul-LR in PME and in Reaction Field (<a href="mailto:pascal.baillod@epfl.ch">pascal.baillod@epfl.ch</a>)<br> 3. aromatic hydrogens (Joanne Hanna)<br> 4. Re: do_dssp error (Miguel Ortiz Lombardia)
<br> 5. RE: RE: Coul-LR in PME and in Reaction Field (Berk Hess)<br> 6. topol.tpr made for 2 nodes while mdrun expected 8<br> (Guillem Plasencia)<br> 7. Re: do_dssp error (Guillem Plasencia)<br> 8. problem in normal mode analysis (arunima singh)
<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Thu, 27 Apr 2006 14:11:30 +0000<br>From: "Guillem Plasencia" <<a href="mailto:guillem_pg@hotmail.com">
guillem_pg@hotmail.com</a>><br>Subject: [gmx-users] Change default "nice" option for mdrun (was: Can<br> not find file: topol.tpr)<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a><br>Message-ID: <<a href="mailto:BAY108-F7C9112D022DD3B7A6B94BF4BD0@phx.gbl">BAY108-F7C9112D022DD3B7A6B94BF4BD0@phx.gbl</a>><br>Content-Type: text/plain; charset=iso-8859-1; format=flowed<br><br>Hello again gmxers,
<br><br>i've found the problem i had (Can not find file: topol.tpr). Silly problem<br>with easy answer, i didn't had a local copy of this file in each node.<br><br>I still have one more question. I'm using 2 boxes with 2 Intel P4 3Ghz
<br>processors (with hyperthreading on), but right now i'm just using only one<br>of them because the other is busy (and it wouldn't be a reliable benchmark).<br><br>I've done the test with lysozyme (cutoff) using only one of the CPUs in one
<br>of my machines, and got the low performance of 3,256 ps /day (it should be<br>1494). I'd like to know how it scalates, by running it using both physical<br>CPUs inside this same machine, but when i do<br><br>grompp <files> -np 2
<br>and<br>mpirun n0 -np 2 mdrun <files> -np 2<br><br>it complains that it was processed for two nodes, not just one. How do i run<br>this job in parallel between the two CPUs in my box? I suppose that if i<br>remove the second node in my LAM-MPI configuration it will still complain
<br>that it was prepared for two nodes, not just one. Also, i've read in the<br>archives that threads aren't yet implemented, so using option -nt 2 doesn't<br>work neither.<br><br>How do i do it?<br><br>Thank you very much !
<br><br>Guillem Plasencia<br><br><br><br><br>------------------------------<br><br>Message: 2<br>Date: Thu, 27 Apr 2006 16:31:48 +0200 (MEST)<br>From: <a href="mailto:pascal.baillod@epfl.ch">pascal.baillod@epfl.ch</a><br>
Subject: [gmx-users] RE: Coul-LR in PME and in Reaction Field<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID: <<a href="mailto:1146148308.4450d5d482cd2@imapwww.epfl.ch">1146148308.4450d5d482cd2@imapwww.epfl.ch
</a>><br>Content-Type: text/plain; charset=ISO-8859-1<br><br>Thank you very much, Berk!<br><br>1) That only leaves one unanswered point, that seems logical but of which I<br>would like to be certain of.. Is there any accessible term in the reaction field
<br>implementation accounting for long-range electrostatic interaction due to the<br>environnement dielectric? Or is this contribution simply added to Coul-SR?<br><br>2) Last, I have a situation that I cannot understand, comparing RF and PME for a
<br>100 residue protein in a water cubic box of roughly 70*70*70A. Comparing<br>contributions of energy groups (g_energy), I obtain:<br><br>-Reaction field: |coul-SR prot-prot| > |coul-SR prot-other|<br>-PME: |coul-SR prot-prot| < |coul-SR prot-other| (the opposite)
<br>(with "||" for absolute values)<br><br>Would that be because of the long-range electrostatic contribution (with the<br>environnement dielectric), added to coul-SR as I suggest in 1)?<br><br>Thank you very much for your help!
<br><br>Pascal<br><br><br><br>*******************************************************************************<br>Pascal Baillod (PhD student)<br>*******************************************************************************
<br>Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322<br>Institute of Chemical Sciences and Engineering , Fax: +41-(0)21-693-0320<br>Laboratory of Computational Chemistry and Biochemistry
<a href="mailto:pascal.baillod@epfl.ch">pascal.baillod@epfl.ch</a><br>Room BCH 4121, Avenue Forel, <a href="http://lcbcpc21.epfl.ch">http://lcbcpc21.epfl.ch</a><br>CH-1015 Lausanne<br>*******************************************************************************
<br><br><br>------------------------------<br><br>Message: 3<br>Date: Thu, 27 Apr 2006 15:29:34 +0100<br>From: "Joanne Hanna" <<a href="mailto:J.F.Hanna@warwick.ac.uk">J.F.Hanna@warwick.ac.uk</a>><br>Subject: [gmx-users] aromatic hydrogens
<br>To: <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:s450e36e.046@liberator.csv.warwick.ac.uk">s450e36e.046@liberator.csv.warwick.ac.uk</a>><br>Content-Type: text/plain; charset=US-ASCII
<br><br>Hi<br><br>I have a question which has been puzzling me regarding the addition of hydrogens to atoms in aromatic rings. I am using force field ffG43a2 but do not have the GROMOS96 manual which is i assume the place to check how the force field was derived (please correct me if i am wrong) and I am confused as to why in a PHE residue all hydrogens (HC) are added to the carbons (C) in the aromatic group but in histidine, these carbon/hydrogen atoms are represented as atom typr CR1. This is mainly in connection to a topology that I have created of AMP, in which I have represented atoms 2C and 8C of the adenine ring as CR1 (on the guidance of Prodrg and the AMP topology in
ffG43a2.rtp) and am now wondering whether these atoms should in fact be represented as explicitly as HC and C.<br>Could any one give me any feedback on any of this and why would be most appropriate to do in line with the ffG43a2 force field.
<br><br>Many thanks<br>Jo<br><br><br><br><br><br><br><br><br><br><br><br>Joanne Hanna<br>Department of Chemistry<br>University of Warwick<br>Coventry<br>CV4 7AL<br><br>(02476) 574623<br><a href="mailto:J.F.Hanna@warwick.ac.uk">
J.F.Hanna@warwick.ac.uk</a><br><br><br>------------------------------<br><br>Message: 4<br>Date: Thu, 27 Apr 2006 16:40:28 +0200<br>From: Miguel Ortiz Lombardia <<a href="mailto:molatwork@yahoo.es">molatwork@yahoo.es</a>
><br>Subject: Re: [gmx-users] do_dssp error<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:4450D7DC.8080302@yahoo.es">
4450D7DC.8080302@yahoo.es</a>><br>Content-Type: text/plain; charset=ISO-8859-1<br><br>-----BEGIN PGP SIGNED MESSAGE-----<br>Hash: SHA1<br><br>Hi Jahan,<br><br>Sorry, I'm not a MSWindows user, so I can't help you here. I think you
<br>can set up a global environment variable somewhere in your control<br>panel, but can't really tell you how.<br><br>Good luck,<br><br><br>Miguel<br><br>jahanshah ashkani wrote:<br>> Thanks for your reply.<br>> I used from Gromacs on WindowsXP with command prompt. How can I change
<br>> DSSP path in this environment? Thank you very much.<br>><br>> Sincerely yours,<br>> Jahan<br>><br>> */Miguel Ortiz Lombardia <<a href="mailto:molatwork@yahoo.es">molatwork@yahoo.es</a>>/* wrote:
<br>><br>> Hi Jahan,<br>><br>> First, you must make sure you have the dssp program; it doesn't come<br>> with gromacs, but you can download it separately from:<br>><br>> <a href="http://swift.cmbi.ru.nl/gv/dssp/">
http://swift.cmbi.ru.nl/gv/dssp/</a><br>><br>> Secondly, if 'setenv' is not working you are not on a csh/tcsh<br>> shell. Try:<br>><br>> export DSSP=/path_to_your_dssp_installation/dssp<br>><br>> This should work if you are on a sh/bash shell.
<br>><br>><br>> HTH,<br>><br>><br>> Miguel<br>><br>><br>> jahanshah ashkani wrote:<br>>> Hi,<br>>> I have a problem with do_dssp command. When I ran it, I found this<br>> fatal<br>
>> error ? DSSP executable does not exist. Then I<br>>> used from setenv DSSP command, but I found this error ?setenv is not<br>>> recognized as an internal or external command,..?<br>>> I would be glad if you help me in this case.
<br>>> Thank you very much.<br>><br>>> Sincerely yours,<br>>> Jahan<br>><br>><br>> ------------------------------------------------------------------------<br>>> Yahoo! Messenger with Voice. Make PC-to-Phone Calls
<br>><br>>> to the US (and 30+ countries) for 2¢/min or less.<br>><br>><br>><br>> ------------------------------------------------------------------------<br>><br>>> _______________________________________________
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</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>> Miguel Ortiz Lombardía<br>> Centro de Investigaciones Oncológicas<br>> C/ Melchor Fernández Almagro, 3
<br>> 28029 Madrid, Spain<br>> Tel. +34 912 246 900<br>> Fax. +34 912 246 976<br>> email: <a href="mailto:molatwork@yahoo.es">molatwork@yahoo.es</a><br>> www: <a href="http://www.ysbl.york.ac.uk/~mol/">http://www.ysbl.york.ac.uk/~mol/
</a><br>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>> Je suis de la mauvaise herbe,<br>> Braves gens, braves gens,<br>> Je pousse en liberté<br>> Dans les jardins mal fréquentés!
<br>> Georges Brassens<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">
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</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>
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</a>><br>> and save big.<br><br><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 list. Use the<br>
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</a><br><br>- --<br>Miguel Ortiz Lombardía<br>Centro de Investigaciones Oncológicas<br>C/ Melchor Fernández Almagro, 3<br>28029 Madrid, Spain<br>Tel. +34 912 246 900<br>Fax. +34 912 246 976<br>email: <a href="mailto:molatwork@yahoo.es">
molatwork@yahoo.es</a><br>www: <a href="http://www.ysbl.york.ac.uk/~mol/">http://www.ysbl.york.ac.uk/~mol/</a><br>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>Je suis de la mauvaise herbe,<br>
Braves gens, braves gens,<br>Je pousse en liberté<br>Dans les jardins mal fréquentés!<br> Georges Brassens<br>-----BEGIN PGP SIGNATURE-----<br>Version: GnuPG v1.4.1 (GNU/Linux)
<br><br>iD8DBQFEUNfcF6oOrDvhbQIRAjsjAJ4qLYO+kYuafFeZ0qmkNi1wAjxMSQCgkSWE<br>TmlDk8MCNXVfjQeXwATvE5M=<br>=cAwL<br>-----END PGP SIGNATURE-----<br><br><br>------------------------------<br><br>Message: 5<br>Date: Thu, 27 Apr 2006 16:49:35 +0200
<br>From: "Berk Hess" <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>><br>Subject: RE: [gmx-users] RE: Coul-LR in PME and in Reaction Field<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a><br>Message-ID: <<a href="mailto:BAY110-F34FC809D2EB0A523397F818EBD0@phx.gbl">BAY110-F34FC809D2EB0A523397F818EBD0@phx.gbl</a>><br>Content-Type: text/plain; format=flowed<br><br><br><br><br>>From: <a href="mailto:pascal.baillod@epfl.ch">
pascal.baillod@epfl.ch</a><br>>Reply-To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a><br>>Subject: [gmx-users] RE: Coul-LR in PME and in Reaction Field<br>>Date: Thu, 27 Apr 2006 16:31:48 +0200 (MEST)<br>><br>>Thank you very much, Berk!<br>><br>>1) That only leaves one unanswered point, that seems logical but of which I
<br>>would like to be certain of.. Is there any accessible term in the reaction<br>>field<br>>implementation accounting for long-range electrostatic interaction due to<br>>the<br>>environnement dielectric? Or is this contribution simply added to Coul-SR?
<br>><br>>2) Last, I have a situation that I cannot understand, comparing RF and PME<br>>for a<br>>100 residue protein in a water cubic box of roughly 70*70*70A. Comparing<br>>contributions of energy groups (g_energy), I obtain:
<br>><br>>-Reaction field: |coul-SR prot-prot| > |coul-SR prot-other|<br>>-PME: |coul-SR prot-prot| < |coul-SR prot-other| (the opposite)<br>>(with "||" for absolute values)<br>><br>
>Would that be because of the long-range electrostatic contribution (with<br>>the<br>>environnement dielectric), added to coul-SR as I suggest in 1)?<br><br>You can not simply compare this terms.<br>Reaction-field is an approximation. It assumes a homogeneous dielectric
<br>medium beyond the cut-off which is clearly not true for your system.<br>Your protein probably has charged residues which cause significant<br>error with RF.<br><br>Secondly the Coul-SR term does not contain 1/r.<br>With RF it is 1/r plus the effect of the reaction field force.
<br>This might be what you call "long-range electrostatic contribution",<br>but it is not really long-range.<br>With PME is it erfc(beta*r)/r.<br><br>Berk.<br><br><br><br><br>------------------------------<br><br>
Message: 6<br>Date: Thu, 27 Apr 2006 15:06:30 +0000<br>From: "Guillem Plasencia" <<a href="mailto:guillem_pg@hotmail.com">guillem_pg@hotmail.com</a>><br>Subject: [gmx-users] topol.tpr made for 2 nodes while mdrun expected 8
<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID: <<a href="mailto:BAY108-F29E7EDC3E10300177C2482F4BD0@phx.gbl">BAY108-F29E7EDC3E10300177C2482F4BD0@phx.gbl</a>><br>Content-Type: text/plain; charset=iso-8859-1; format=flowed
<br><br>Hello gmxers,<br><br>i've been struggling to make gromacs be able to use my 2 Dual CPU machines,<br>without success.<br>I'd like to know exactly how to configure lam and how to preprocess with<br>grompp (and then execute with mpirun) in order to be able to run as many
<br>parallel processes in my 2 Dual CPU machines that sum 4 CPUs (8 with<br>hyperthreading).<br><br>My lam configuration file content is:<br>lead7 cpu=4<br><a href="http://192.168.1.9">192.168.1.9</a> cpu=4<br><br>As a short brief, i've been able to run the same lisozyme cutoff benchmark
<br>in 4 parallel processes in only one node by commenting out the first line<br>(the one which begins ..lead7) in my lam configuration file, and then<br><br>preprocessing as:<br>grompp -f cutoff.mdp -c conf.gro -p topol.top
-np 4 -shuffle -sort<br><br>and running with:<br>mpirun C mdrun -s topol.tpr -nice 0 -np 4<br><br>So far, everything worked fine.<br><br>Problems arises when i try to include the other node (lead7).<br><br>I preprocess benchmarck lisozyme with cutoff as follows:
<br>grompp -f cutoff.mdp -c conf.gro -p topol.top -np 8 -shuffle -sort<br><br>I include -np 8 to split into 8 processes (is that ok?)<br><br>but when i do<br><br>mpirun C mdrun -s topol.tpr -nice 0 -np 8<br><br>i get the error:
<br><br>Reading file topol.tpr, VERSION 3.3.1 (single precision)<br>-------------------------------------------------------<br>Program mdrun, VERSION 3.3.1<br>Source code file: init.c, line: 69<br><br>Fatal error:<br>run input file
topol.tpr was made for 2 nodes,<br> while mdrun expected it to be for 8 nodes.<br>-------------------------------------------------------<br><br>How can be that, if i used grompp with option -np 8 ?<br><br>Any idea on how can i do it?
<br><br>Thank you very much for your help,<br><br>Guillem Plasencia<br>Spain<br><br><br><br><br>------------------------------<br><br>Message: 7<br>Date: Thu, 27 Apr 2006 15:13:52 +0000<br>From: "Guillem Plasencia" <
<a href="mailto:guillem_pg@hotmail.com">guillem_pg@hotmail.com</a>><br>Subject: Re: [gmx-users] do_dssp error<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID: <<a href="mailto:BAY108-F3283C95128C72BB90D40EAF4BD0@phx.gbl">
BAY108-F3283C95128C72BB90D40EAF4BD0@phx.gbl</a>><br>Content-Type: text/plain; charset=iso-8859-1; format=flowed<br><br>Hello Jahan,<br><br>in WindowsXP, to set an environment variable, go to control panel (select<br>classic view on the left pane), then select "System" icon.. Select "Advanced
<br>Options Tab", then select "Environment Variables" in the bottom.<br><br>Hope this helps,<br><br>Guillem Plasencia<br>Spain.<br><br><br>>jahanshah ashkani wrote:<br>> > Thanks for your reply.<br>
> > I used from Gromacs on WindowsXP with command prompt. How can I change<br>> > DSSP path in this environment? Thank you very much.<br>> ><br>> > Sincerely yours,<br>> > Jahan<br><br><br><br>
<br>------------------------------<br><br>Message: 8<br>Date: 27 Apr 2006 15:54:52 -0000<br>From: "arunima singh" <<a href="mailto:arunima555@rediffmail.com">arunima555@rediffmail.com</a>><br>Subject: [gmx-users] problem in normal mode analysis
<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID: <<a href="mailto:20060427155452.13421.qmail@webmail45.rediffmail.com">20060427155452.13421.qmail@webmail45.rediffmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br><br> <br>hi,<br>I m running normal mode on 8 processors for Lysozyme but it runs only 1293 steps out of 22497 and ends with the message "MPI process rank 0 <n0, p17548> caught a SIGSEGV".
<br>Please tell me how to build the hessian gor NM.<br>Arunima<br><br><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20060427/53f9c036/attachment.html">
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<br></blockquote></div><br><br clear="all"><br>-- <br>Mohan Boggara<br>Graduate Research Assistant<br>Department of Chemical Engineering<br>University of Houston<br>S222 Engineering Bldg 1<br>Houston, Texas-77204, USA<br>
Mobile: 1-713-259-2166<br>Office: 1-713-743-4314 <br><a href="http://polymer.chee.uh.edu/">http://polymer.chee.uh.edu/</a><br><br>All human actions have one or more of these seven causes: chance, nature, compulsion, habit, reason, passion, and desire.-- Aristotle