[gmx-users] angular velocity autocorrelation
Dear Users, I need to calculate the angular velocity correlation function. From the gromacs discussion forum, I understand that one should be able to use g_rotacf to calculate the angular velocity correlation function ( http://oldwww.gromacs.org/pipermail/gmx-users/2004-September/012278.html). However, when I look into the g_rotacf function, if I am not mistaken, the rotational correlation function gives us the autocorrelation of the normal vector to the two vectors defined in the input. It does not provide the angular velocity correlation function. Could someone give me pointers as to how one can calculate the angular velocity correlation function from g_rotacf? I need this information to analyze the density of states distribution. Any help is greatly appreciated. Thank you, Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] segmentation fault: g_velacc
Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] segmentation fault: g_velacc
Thanks very much, Dr. Kutzner! On Tue, Feb 1, 2011 at 9:14 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Vigneshwar, the problem is fixed now in the release-4-0-patches branch. Carsten On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote: Hi, apparently this bug fix made it to 4.5, but not to 4.0. I will apply the fix also there. Carsten On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Either apply the patch or upgrade to a newer version of Gromacs that contains this bug fix. -Justin Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] on calculation of the atomic covariance
Dear Tsjerk, Thanks very much. Yes, true, difference in the ranges of the covariances means there is difference between the two systems. I did try the modified g_covar in the contribution section but couldn't make it work first, but I realized it worked only for GROMACS ver 3.3.3. Now, I am able to calculate the correlation matrix. Thanks very much for all your help and pointers. Sincerely, Vignesh On Thu, Nov 11, 2010 at 4:49 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vignesh, If your covariances show different ranges, isn't that a difference between your systems, wild-type and mutated? Then again, there's also noise in the covariances (noise in the fluctuations, ergo noise in the noise ;)). The rest might be comparable, making scaling based on the extremes seem like a bad idea. You might be better of calculating correlations, rather than covariances. There's a modified g_covar in the contributions section of the gromacs site for calculating those. Cheers, Tsjerk On Thu, Nov 11, 2010 at 3:53 AM, Vigneshwar Ramakrishnan vmsrvign...@gmail.com wrote: Dear All, I tried using the xpm2ps -combine option to plot the two matrices in the same plot. xpm2ps -f covara_cognate.xpm -f2 covara_G5C.xpm -diag none -combine halves -cmin -0.5 -cmax 0.8 However, I still get two legends and each of the matrices are scaled differently. That is, the output range is NOT combined, as the -combine option is supposed to do. I tried different options (add, sub, div ; with and without the -cmin and -cmax options etc) I am sure I am missing something here. May I please know if anybody got it worked, and if so, can help me out? Thanks very much, Vignesh On Thu, Nov 11, 2010 at 10:12 AM, Vigneshwar Ramakrishnan vmsrvign...@gmail.com wrote: Thanks very much, Justin. Somehow this thread did not come up during my search. Really appreciate your help. Sincerely, Vignesh On Wed, Nov 10, 2010 at 10:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: There are two relevant threads on this same topic that will likely provide some insight (particularly the second): http://lists.gromacs.org/pipermail/gmx-users/2009-November/046846.html http://lists.gromacs.org/pipermail/gmx-users/2009-November/046854.html -Justin Vigneshwar Ramakrishnan wrote: Dear All, I am trying to study the effect of single-point mutations on correlated motions in a protein-DNA system. I am able to calculate the atomic covariance matrix using the g_covar -xpma option. However, when I try to compare the covariance matrices for the two systems (to study the effect of the mutation), I find that the output is not scaled identically. That is, in one of the systems the atomic covariance varies between -0.04 and +0.5 whereas in the other it varies between -0.1 and +0.4. Now, this means that I cannot compare the two systems immediately from the eps file output (obtained after xpm2ps). Could anybody please tell me if there is a way to plot the output on identical scales (say, -1 to +1, or any other scale) using GROMACS? The other way, I understand is to use the ascii output of g_covar and use the values to create the covariance plot using softwares like MATLAB which can rescale the image colors. However, for this, one needs to calculate the atomic covariance from the ascii output (which is x1x1,x1y1,x1z1 etc). From the manual, I understand that the way to calculate atomic covariance is for each atom pair the sum of the xx, yy and zz covariances. Am I right if I understand that this means: atomic cov (X1) = x1x1 + y1y1 + z1z1 atomic cov (X2) = x2x2 + y2y2 + z2z2 ... I greatly appreciate any help or pointers. Thanks very much, Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore
[gmx-users] on calculation of the atomic covariance
Dear All, I am trying to study the effect of single-point mutations on correlated motions in a protein-DNA system. I am able to calculate the atomic covariance matrix using the g_covar -xpma option. However, when I try to compare the covariance matrices for the two systems (to study the effect of the mutation), I find that the output is not scaled identically. That is, in one of the systems the atomic covariance varies between -0.04 and +0.5 whereas in the other it varies between -0.1 and +0.4. Now, this means that I cannot compare the two systems immediately from the eps file output (obtained after xpm2ps). Could anybody please tell me if there is a way to plot the output on identical scales (say, -1 to +1, or any other scale) using GROMACS? The other way, I understand is to use the ascii output of g_covar and use the values to create the covariance plot using softwares like MATLAB which can rescale the image colors. However, for this, one needs to calculate the atomic covariance from the ascii output (which is x1x1,x1y1,x1z1 etc). From the manual, I understand that the way to calculate atomic covariance is for each atom pair the sum of the xx, yy and zz covariances. Am I right if I understand that this means: atomic cov (X1) = x1x1 + y1y1 + z1z1 atomic cov (X2) = x2x2 + y2y2 + z2z2 ... I greatly appreciate any help or pointers. Thanks very much, Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] on calculation of the atomic covariance
Thanks very much, Justin. Somehow this thread did not come up during my search. Really appreciate your help. Sincerely, Vignesh On Wed, Nov 10, 2010 at 10:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: There are two relevant threads on this same topic that will likely provide some insight (particularly the second): http://lists.gromacs.org/pipermail/gmx-users/2009-November/046846.html http://lists.gromacs.org/pipermail/gmx-users/2009-November/046854.html -Justin Vigneshwar Ramakrishnan wrote: Dear All, I am trying to study the effect of single-point mutations on correlated motions in a protein-DNA system. I am able to calculate the atomic covariance matrix using the g_covar -xpma option. However, when I try to compare the covariance matrices for the two systems (to study the effect of the mutation), I find that the output is not scaled identically. That is, in one of the systems the atomic covariance varies between -0.04 and +0.5 whereas in the other it varies between -0.1 and +0.4. Now, this means that I cannot compare the two systems immediately from the eps file output (obtained after xpm2ps). Could anybody please tell me if there is a way to plot the output on identical scales (say, -1 to +1, or any other scale) using GROMACS? The other way, I understand is to use the ascii output of g_covar and use the values to create the covariance plot using softwares like MATLAB which can rescale the image colors. However, for this, one needs to calculate the atomic covariance from the ascii output (which is x1x1,x1y1,x1z1 etc). From the manual, I understand that the way to calculate atomic covariance is for each atom pair the sum of the xx, yy and zz covariances. Am I right if I understand that this means: atomic cov (X1) = x1x1 + y1y1 + z1z1 atomic cov (X2) = x2x2 + y2y2 + z2z2 ... I greatly appreciate any help or pointers. Thanks very much, Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] on calculation of the atomic covariance
Dear All, I tried using the xpm2ps -combine option to plot the two matrices in the same plot. xpm2ps -f covara_cognate.xpm -f2 covara_G5C.xpm -diag none -combine halves -cmin -0.5 -cmax 0.8 However, I still get two legends and each of the matrices are scaled differently. That is, the output range is NOT combined, as the -combine option is supposed to do. I tried different options (add, sub, div ; with and without the -cmin and -cmax options etc) I am sure I am missing something here. May I please know if anybody got it worked, and if so, can help me out? Thanks very much, Vignesh On Thu, Nov 11, 2010 at 10:12 AM, Vigneshwar Ramakrishnan vmsrvign...@gmail.com wrote: Thanks very much, Justin. Somehow this thread did not come up during my search. Really appreciate your help. Sincerely, Vignesh On Wed, Nov 10, 2010 at 10:23 PM, Justin A. Lemkul jalem...@vt.eduwrote: There are two relevant threads on this same topic that will likely provide some insight (particularly the second): http://lists.gromacs.org/pipermail/gmx-users/2009-November/046846.html http://lists.gromacs.org/pipermail/gmx-users/2009-November/046854.html -Justin Vigneshwar Ramakrishnan wrote: Dear All, I am trying to study the effect of single-point mutations on correlated motions in a protein-DNA system. I am able to calculate the atomic covariance matrix using the g_covar -xpma option. However, when I try to compare the covariance matrices for the two systems (to study the effect of the mutation), I find that the output is not scaled identically. That is, in one of the systems the atomic covariance varies between -0.04 and +0.5 whereas in the other it varies between -0.1 and +0.4. Now, this means that I cannot compare the two systems immediately from the eps file output (obtained after xpm2ps). Could anybody please tell me if there is a way to plot the output on identical scales (say, -1 to +1, or any other scale) using GROMACS? The other way, I understand is to use the ascii output of g_covar and use the values to create the covariance plot using softwares like MATLAB which can rescale the image colors. However, for this, one needs to calculate the atomic covariance from the ascii output (which is x1x1,x1y1,x1z1 etc). From the manual, I understand that the way to calculate atomic covariance is for each atom pair the sum of the xx, yy and zz covariances. Am I right if I understand that this means: atomic cov (X1) = x1x1 + y1y1 + z1z1 atomic cov (X2) = x2x2 + y2y2 + z2z2 ... I greatly appreciate any help or pointers. Thanks very much, Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] converting parmbsc0 dihedrals to RB function
Dear Dr. Mark, Thanks very much for pointing out that GROMACS can handle multiple instances of the parameters with different n for a single dihedral. However, given that, in the existing ffamber ports in GROMACS the other dihedral parameters have been converted to RB form, would it make a difference to just import these new parameters in the non-RB form? To my knowledge, the torsional term should not vary (or, vary within acceptable limits) irrespective of the functional form used to calculate it. But I would like to know if there could be some reason for which this assumption cannot be made. Dear Dr. Alan, Thanks very much for pointing out to the acpypi code. I was able to better understand the conversion procedure. Sincerely, Vignesh On Wed, Apr 7, 2010 at 10:04 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote: Dear Users, I am trying to port the new parmbsc0 forcefield (http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA simulations. While unit conversions are sufficient to convert many of the parameters from AMBER to GROMACS format, dihedral angle conversion does not seem to be straight forward - the dihedral parameters need to be converted to the Ryckaert-Bellemans parameters. Why? GROMACS can probably do the non-RB form - IIRC you can implement a sum of multiple instances of 4.61 with different n. I went through the GROMACS 4.0 manual, especially equations 4.61-4.65 to understand the procedure. The procedure involves comparing the fourier expansion of the IUPAC convention of dihedral potential (equation 4.65) with the Ryckaert-Bellemans (RB) functional of dihedral potential (equation 4.62) to get the Cn's of the RB function. However, I am not able to understand how to account for the phase angles. (Also to note, the parmbsc0 forcefield contains phase angles other than 0 and 180.) Elegant conversion formulae require those angles to be convenient... Mark Any advice or suggestion will be of great help. Thank you, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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 -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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] converting parmbsc0 dihedrals to RB function
Dear Users, I am trying to port the new parmbsc0 forcefield ( http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA simulations. While unit conversions are sufficient to convert many of the parameters from AMBER to GROMACS format, dihedral angle conversion does not seem to be straight forward - the dihedral parameters need to be converted to the Ryckaert-Bellemans parameters. I went through the GROMACS 4.0 manual, especially equations 4.61-4.65 to understand the procedure. The procedure involves comparing the fourier expansion of the IUPAC convention of dihedral potential (equation 4.65) with the Ryckaert-Bellemans (RB) functional of dihedral potential (equation 4.62) to get the Cn's of the RB function. However, I am not able to understand how to account for the phase angles. (Also to note, the parmbsc0 forcefield contains phase angles other than 0 and 180.) Any advice or suggestion will be of great help. Thank you, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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] question regarding genion
Hi Sarbani, I think you should use genion -random no along with other options. Thanks, Vignesh On Fri, Sep 12, 2008 at 3:30 PM, sarbani chattopadhyay [EMAIL PROTECTED] wrote: Hi everybody, I want to place my counterions close to the charged amino acids. I am aware of the fact that even if the counterions are randomly added yet they will eventually settle during equlibration. But still I will like to start with a structure that has counterions close to charged residues. I have been going through the archive and the manual but I could not figure out how to disable the default option of -random while using the genion command. Can anyone guide me through the command that is required to add counterions based on potential so that the counterions are closed to the charged residues? Thanks in advance Sarbani [image: Ebay]http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! The rewards of sincere resolves are highs money can never buy! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ffamber and ions
hi Alan, Can you show us your modified ions.itp file (just the Cl part) and the exact command options you used for genion? Thanks, Vignesh On Thu, Jul 3, 2008 at 2:44 PM, Alan [EMAIL PROTECTED] wrote: Hi List, To people using ffamber. I have ffamber with ions.itp modified to recognise ffamber ions. All seems fine and working. So, I have a protein, net charge +4 e. In the pdb file there no ions and no water. I modify the pdb as said in ffamber instructions. All fine. Then, I add water and hence I use genion to neutralise my system. I add 4 Cl. All fine. However when using grompp for preparing the inputs for a minimisation, I got a warning saying that my system is now +8 e. It happens no matter what ion I use with ffamber (being it pos or neg, or value 2). It's like if genion were counting only the ions and not reading the ion's charge value. I know it's reading my modified ions.itp file because otherwise genion will fail to process. Has someone else seen that? Any comments? Despite this, I can minimise and carry on MD on my system. Is there any other to definitely know if GMX is computing the right charge values? Many thanks in advance. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! The rewards of sincere resolves are highs money can never buy! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Terminal specification for DNA in Gro96 ff
Dear All, I am trying to simulate a protein-DNA system using Gromos96 53a6 forcefield. Could anybody tell me how to specify the terminals for DNA? There is no termini database entry for DNA for this forcefield. Thank you, Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! The rewards of sincere resolves are highs money can never buy! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] system contains proteins and DNAs with ffamber99
hi, I think the answer to both of your questions is YES! Though, I have used ffamber03 for simulating protein+DNA. But I guess it shouldn't matter. Regards, Vignesh On Wed, Jun 11, 2008 at 3:50 PM, Dechang Li [EMAIL PROTECTED] wrote: Dear all, Sometimes,the PDB file contains water molecules which only have the oxygen atom. Can Gromacs add the hydrogen atoms of the water molecules? Additionly, when use Gromacs with the force field ffamber99, Can it add the hydrogen atoms of the DNA? Can I use the force field ffamber99 to simulate the system which contains proteins and DNAs? Best regards, = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! The rewards of sincere resolves are highs money can never buy! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Simulating Protein+Dextran/PEG
Dear All, I am a newbie to GROMACS and to MD simulations. I want to simulate and study protein in the presence of Dextran or PEG. 1. From literature and internet searches, I understand that PEG topology file can be generated using the PRODRG server and hence protein+PEG simulations should be possible. But what I am worried is that, the GROMACS forcefields are united atom models. So will I then not be able to study hydrogen bonding in my system? 2. For Dextran, I understand from literature that CHARMM forcefield can be used. I also understand that there are perl scripts to convert the charmm input files into gromacs compatible versions. But can anyone tell me if the perl script available from the GROMACS-user contribution section can handle Dextran? It says that it accurately handles Lipids and silicates but there is no comment about dextran or carbohydrates. I will be grateful for any suggestions and directions. Thank you, Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! The rewards of sincere resolves are highs money can never buy! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] adding missing hydrogen in PDB files
Hi All, I am a newbie to GROMACS, so pardon me if I am wrong. I think pdb2gmx can handle this with amber forcefields. We just need to use the right nomenclature. I think the .hdb files for amber ff in GROMACS are already equipped with the necessary info. I am not sure why one must use an external software for adding the hydrogen atoms. If I am wrong, pls correct me. Thank you, Vignesh On Fri, May 2, 2008 at 12:09 AM, Justin A. Lemkul [EMAIL PROTECTED] wrote: In terms of external software, check out OpenBabel: http://openbabel.org/wiki/Main_Page There's also the H++ server, which employs Babel as part of its algorithm: http://biophysics.cs.vt.edu/H++/index.php I believe H++ can handle nucleic acids. You could also do all of this with Gromacs, if you can come up with relevant entries in the .hdb file for your particular force field. Then pdb2gmx could produce the right structure with added hydrogens. -Justin Quoting Arijit Maitra [EMAIL PROTECTED]: Hi All I have been trying to simulate a DNA tetramer d()_2 using gromacs with amber ports. I have downloaded the X-ray structure from www.rcsb.org/pdb which has several missing hydrogen atoms. Can anybody advise how to plug in the missing atoms, e.g. with softwares or otherwise to proceed with the pdb2gmx command? Thanks Ari Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! The rewards of sincere resolves are highs money can never buy! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
