[gmx-users] Shell dynamics with vdW terms.
Hello, I have some troubles understanding the way used by Gromacs in optimizing the position of shells. In section 3.5.1 the manual says that the force on a shell particle is decomposed into two terms. The first represents the polarization and the second includes the Coulomb and van der Waals interactions. It continues assuming that the second term is constant and derives an analytic expression to calculate the shell position. My troubles arise after reading the paper: J. Phys. Chem. B 2009, 113, 7270-7281 by A. Villa, B. Hess H. Saint-Martin. In the paper they simulate Lanthanides in water. In Table 2 they assign a 1/r**12 term to the ion-shell - water-shell interaction (the A_MIM parameter). I believe that this term is used in eq. 8 of the Supporting Information. Because is vdW like it seems to me that it breaks the previously mentioned assumption of vdW constancy. Could anybody help me? Thanks a lot. Rafael -- Dr. Rafael R. Pappalardo Dept. of Physical Chemistry, Univ. de Sevilla (Spain) e-mail: raf...@us.es ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Shell dynamics with vdW terms.
Hi, The equation you refer to is only an initial guess for the optimization. The positions of the shells are optimized using the forces from the full potential function. Berk From: raf...@us.es To: gmx-users@gromacs.org Date: Tue, 9 Jun 2009 09:51:13 +0200 Subject: [gmx-users] Shell dynamics with vdW terms. Hello, I have some troubles understanding the way used by Gromacs in optimizing the position of shells. In section 3.5.1 the manual says that the force on a shell particle is decomposed into two terms. The first represents the polarization and the second includes the Coulomb and van der Waals interactions. It continues assuming that the second term is constant and derives an analytic expression to calculate the shell position. My troubles arise after reading the paper: J. Phys. Chem. B 2009, 113, 7270-7281 by A. Villa, B. Hess H. Saint-Martin. In the paper they simulate Lanthanides in water. In Table 2 they assign a 1/r**12 term to the ion-shell - water-shell interaction (the A_MIM parameter). I believe that this term is used in eq. 8 of the Supporting Information. Because is vdW like it seems to me that it breaks the previously mentioned assumption of vdW constancy. Could anybody help me? Thanks a lot. Rafael -- Dr. Rafael R. Pappalardo Dept. of Physical Chemistry, Univ. de Sevilla (Spain) e-mail: raf...@us.es ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in running grompp
--- On Mon, 8/6/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] problem in running grompp To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, 8 June, 2009, 4:47 PM Samik Bhattacharya wrote: hi i am simulating a membrane protein in POPC bilayer and for that i am following justin's tutorial.it's a nice tutorial and is really helpful. but i'm facing some problems in running the grompp command. after the solvation when i am going to run grompp, it is generting an error as follows ''Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 843 Fatal error: Atomtype CA not found'' but is not CA the main chain alpha carbon...why is not grompp taking CA then? i can't make out where the problem lies? i little help on this shall be very encouraging. If you're seeing this error, then you've done something wrong when combining lipid.itp with the Gromos force field file. -Justin Thank You Shamik Thank you Justin for the answar. but now how to solve it? where should i make changes to correct that? pls let me know what to do... waiting for your answar Thank you again.. ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Own a website.Get an unlimited package.Pay next to nothing.*Go to http://in.business.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in running grompp
Samik Bhattacharya wrote: Thank you Justin for the answar. but now how to solve it? where should i make changes to correct that? pls let me know what to do... waiting for your answar Thank you again.. CA is not an alpha-carbon, it is a ffgmx atom type. So, therefore, you have copies some ffgmx parameters into the ffG53a6nb_lipid.itp that the tutorial describes, probably from the ;; parameters for lipid-GROMOS interactions which the tutorial clearly tells you to delete. -Justin ___ gmx-users mailing listgmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! http://in.rd.yahoo.com/tagline_Travel_1/*http://in.travel.yahoo.com/ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] trouble for old/new GROMACS site
Hi all, probably this is a very trivial question: how can I find information in the GROMACS site? I'm quite in trouble because I'm trying to search for some information in the gmx-user archive, and I can't reach it neither in the old GROMACS site nor in the new one. I supposed I had to register to see the content of the site, and I did it, but still I don't see anything in the two sites. Can anyone help me? Thank you Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo...@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you are too small to make a difference, try sleeping with a mosquito ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trouble for old/new GROMACS site
Anna Marabotti wrote: Hi all, probably this is a very trivial question: how can I find information in the GROMACS site? I'm quite in trouble because I'm trying to search for some information in the gmx-user archive, and I can't reach it neither in the old GROMACS site nor in the new one. I supposed I had to register to see the content of the site, and I did it, but still I don't see anything in the two sites. Can anyone help me? Everything is still available at oldwww.gromacs.org; it seems to be working fine right now. The search page, for example, is at: http://oldwww.gromacs.org/swish-e/search/search2.php -Justin Thank you Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo...@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you are too small to make a difference, try sleeping with a mosquito ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Shell dynamics with vdW terms.
On Tuesday 09 June 2009 10:02:47 Berk Hess wrote: Hi, The equation you refer to is only an initial guess for the optimization. The positions of the shells are optimized using the forces from the full potential function. Berk From: raf...@us.es To: gmx-users@gromacs.org Date: Tue, 9 Jun 2009 09:51:13 +0200 Subject: [gmx-users] Shell dynamics with vdW terms. Hello, I have some troubles understanding the way used by Gromacs in optimizing the position of shells. In section 3.5.1 the manual says that the force on a shell particle is decomposed into two terms. The first represents the polarization and the second includes the Coulomb and van der Waals interactions. It continues assuming that the second term is constant and derives an analytic expression to calculate the shell position. My troubles arise after reading the paper: J. Phys. Chem. B 2009, 113, 7270-7281 by A. Villa, B. Hess H. Saint-Martin. In the paper they simulate Lanthanides in water. In Table 2 they assign a 1/r**12 term to the ion-shell - water-shell interaction (the A_MIM parameter). I believe that this term is used in eq. 8 of the Supporting Information. Because is vdW like it seems to me that it breaks the previously mentioned assumption of vdW constancy. Could anybody help me? Thanks a lot. Rafael -- Dr. Rafael R. Pappalardo Dept. of Physical Chemistry, Univ. de Sevilla (Spain) e-mail: raf...@us.es ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx Dear Berk, thanks for the quick answer. I am having lot of troubles trying to minimize a cation+1 water molecule using Gromacs 4.0.5. The minimization proceeds without warnings but at a certain point it seems that the shell minimizer does not work ok. The kind of structures I am obtaining are: Generated by trjconv : Cf in Water t= 9.0 6 1Cf_sCf1 1.49566 1.61167 1.73228 1Cf_sMs2 1.49450 1.62107 1.72892 2SOL OW3 1.51913 1.41088 1.80113 2SOLHW14 1.51596 1.36681 1.89843 2SOLHW25 1.53786 1.31814 1.75093 2SOL MW6 1.51789 1.42144 1.79730 3.10740 3.10740 3.10740 Generated by trjconv : Cf in Water t= 10.0 6 1Cf_sCf1 1.49838 1.58947 1.74003 1Cf_sMs2 1.49587 1.60861 1.73299 2SOL OW3 1.51772 1.42189 1.79765 2SOLHW14 1.51568 1.37036 1.89631 2SOLHW25 1.53733 1.32238 1.75035 2SOL MW6 1.51602 1.43730 1.79166 3.10740 3.10740 3.10740 Generated by trjconv : Cf in Water t= 11.0 6 1Cf_sCf1 1.50510 1.52690 1.75928 1Cf_sMs2 1.50102 1.57015 1.74742 2SOL OW3 1.51647 1.43148 1.79236 2SOLHW14 1.51461 1.38178 1.89116 2SOLHW25 1.53582 1.33543 1.74711 2SOL MW6 1.50797 1.50425 1.77168 3.10740 3.10740 3.10740 I see no warning or error in the md.log file albeit the Coulomb energy is rather large. The run continues at to t=50.000 with the message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 0.1 Could I sent you the input files in order to get some advice? Best regards, Rafael -- Dr. Rafael R. Pappalardo Dept. of Physical Chemistry, Univ. de Sevilla (Spain) e-mail: raf...@us.es ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Shell dynamics with vdW terms.
From: raf...@us.es To: gmx-users@gromacs.org Subject: Re: [gmx-users] Shell dynamics with vdW terms. Date: Tue, 9 Jun 2009 16:29:39 +0200 On Tuesday 09 June 2009 10:02:47 Berk Hess wrote: Hi, The equation you refer to is only an initial guess for the optimization. The positions of the shells are optimized using the forces from the full potential function. Berk From: raf...@us.es To: gmx-users@gromacs.org Date: Tue, 9 Jun 2009 09:51:13 +0200 Subject: [gmx-users] Shell dynamics with vdW terms. Hello, I have some troubles understanding the way used by Gromacs in optimizing the position of shells. In section 3.5.1 the manual says that the force on a shell particle is decomposed into two terms. The first represents the polarization and the second includes the Coulomb and van der Waals interactions. It continues assuming that the second term is constant and derives an analytic expression to calculate the shell position. My troubles arise after reading the paper: J. Phys. Chem. B 2009, 113, 7270-7281 by A. Villa, B. Hess H. Saint-Martin. In the paper they simulate Lanthanides in water. In Table 2 they assign a 1/r**12 term to the ion-shell - water-shell interaction (the A_MIM parameter). I believe that this term is used in eq. 8 of the Supporting Information. Because is vdW like it seems to me that it breaks the previously mentioned assumption of vdW constancy. Could anybody help me? Thanks a lot. Rafael -- Dr. Rafael R. Pappalardo Dept. of Physical Chemistry, Univ. de Sevilla (Spain) e-mail: raf...@us.es ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx Dear Berk, thanks for the quick answer. I am having lot of troubles trying to minimize a cation+1 water molecule using Gromacs 4.0.5. The minimization proceeds without warnings but at a certain point it seems that the shell minimizer does not work ok. The kind of structures I am obtaining are: Generated by trjconv : Cf in Water t= 9.0 6 1Cf_sCf1 1.49566 1.61167 1.73228 1Cf_sMs2 1.49450 1.62107 1.72892 2SOL OW3 1.51913 1.41088 1.80113 2SOLHW14 1.51596 1.36681 1.89843 2SOLHW25 1.53786 1.31814 1.75093 2SOL MW6 1.51789 1.42144 1.79730 3.10740 3.10740 3.10740 Generated by trjconv : Cf in Water t= 10.0 6 1Cf_sCf1 1.49838 1.58947 1.74003 1Cf_sMs2 1.49587 1.60861 1.73299 2SOL OW3 1.51772 1.42189 1.79765 2SOLHW14 1.51568 1.37036 1.89631 2SOLHW25 1.53733 1.32238 1.75035 2SOL MW6 1.51602 1.43730 1.79166 3.10740 3.10740 3.10740 Generated by trjconv : Cf in Water t= 11.0 6 1Cf_sCf1 1.50510 1.52690 1.75928 1Cf_sMs2 1.50102 1.57015 1.74742 2SOL OW3 1.51647 1.43148 1.79236 2SOLHW14 1.51461 1.38178 1.89116 2SOLHW25 1.53582 1.33543 1.74711 2SOL MW6 1.50797 1.50425 1.77168 3.10740 3.10740 3.10740 I see no warning or error in the md.log file albeit the Coulomb energy is rather large. The run continues at to t=50.000 with the message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 0.1 Could I sent you the input files in order to get some advice? Best regards, Rafael -- Dr. Rafael R. Pappalardo Dept. of Physical Chemistry, Univ. de Sevilla (Spain) e-mail: raf...@us.es At this point I have no clue if there might be something wrong at all. There are many questions to ask: What energies would you expect? Have you checked if the minimized structure looks reasonable? Is this a force field from the literature that it proven to work with this water model? Polarizable models are tricky, if there is not enough repulsion or the spring constant is too weak you can easily get a polarization catastrophe. Berk _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org
[gmx-users] units of eigenvalues of mass-weighted covariance matrix
Dear all, I am confused on the units of the eigenvalues calculated from g_covar of mass-weighted covariance matrix. From the output, it says the unit is (nm\S2\N) but from my understanding, it is supposed to be kg/m2. Thanks for advance for any comments. Regards, Qin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] non-standard residues in pdb2gmx
Gard Nelson wrote: Hey everyone, I have a .pdb file that I need to convert to .gmx. The tricky thing is that the protein has a lipid bound to the N-terminus, which pdb2gmx doesn't recognize. The lipid is a myristic acid residue (14:0), and I haven't been able to find it in any database. What would be the most straightforward way to get pdb2gmx to recognize this structure? I plan on using multiple monomers in the future, so I'd rather not manually alter the .top file. I've been looking at modifying the .rtp file to include this residue, but then I'm wondering how to parameterize it. If anyone has any suggestions aobut any of this, I'd be really happy to hear it. If you want pdb2gmx to recognize it, then the .rtp is the only way to do it. As for parameterization, see the standard advice: http://oldwiki.gromacs.org/index.php/Parameterization What might be even easier is to create an .itp file for myristic acid, so you can #include myristic.itp in any topology that needs it. That way you don't have to mess with .rtp files, or run pdb2gmx for every system that contains myristic acid. It's essentially the same amount of work to create an .itp file as it is to make an .rtp entry - the real work is in parameterization! -Justin Thanks, Gard ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] units of eigenvalues of mass-weighted covariance matrix
Wang Qin wrote: Dear all, I am confused on the units of the eigenvalues calculated from g_covar of mass-weighted covariance matrix. From the output, it says the unit is (nm\S2\N) but from my understanding, it is supposed to be kg/m2. Various of the GROMACS analysis tools don't write the correct units in .xvg output. This looks like such a case. There's a section early in the manual that describes the GROMACS unit conventions, from which you should be able to deduce what the units are. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
