Re: [gmx-users] make_ndx
sarbani chattopadhyay wrote: hi, I want to select two groups in the index file, one group consisting of only the aromatic ring of phenylalanine and the other group consisting of only the alpha carbon. I want to know the way to use the make_ndx command for this. After entering make_ndx, you can use hRETURN to get some primitive help. In this case, you can most quickly solve your problem by hand-editing. See http://wiki.gromacs.org/index.php/Index_File Mark ___ 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: Re: [gmx-users] make_ndx
Thanks Mark, I could do it following your suggestion. Sarbani On Wed, 24 Oct 2007 Mark Abraham wrote : sarbani chattopadhyay wrote: hi, I want to select two groups in the index file, one group consisting of only the aromatic ring of phenylalanine and the other group consisting of only the alpha carbon. I want to know the way to use the make_ndx command for this. After entering make_ndx, you can use hRETURN to get some primitive help. In this case, you can most quickly solve your problem by hand-editing. See http:// wiki.gromacs.org/index.php/Index_File Mark ___ 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 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] missing Ryckaert-Bell in 3.3.2 is now considered asERROR?
From: Martin Höfling [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: [gmx-users] missing Ryckaert-Bell in 3.3.2 is now considered asERROR? Date: Wed, 24 Oct 2007 00:14:55 +0200 Hi all, has the default behaviour of 3.3.1 - 3.3.2 changed from Warning to Errors concerning this?: AFAIR in 3.3.1 WARNING ... No default Ryckaert-Bell. types, using zeroes to: ERROR 1 [file topol.top, line 159]: No default Ryckaert-Bell. types in 3.3.2 Yes. We should have done this years ago, but I wasn't really aware of this issue, since I always make proper topologies :) The new -zero option of grompp changes the behavior back to the old one. Berk. _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ 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] surface tension calculation in g_energy
Hi all, I use the option #Surf*SurfTens in g_engery to calculate the surface tension, but I find that I really do not know how it works after I get some inconsistent results compared with the calculation using the formula gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz ( there are two surfaces here and the surfaces in normal to the Z-axis). Energy Average RMSD Fluct. Drift Tot-Drift --- #Surf*SurfTen1136.52557.05 2557 0.00852598 51.1559 == ### == A V E R A G E S == ### == Pressure (bar) -1.93061e+02 -6.88599e-01 -1.66823e-02 -6.84564e-01 -1.93953e+02 -2.93803e-02 7.79006e-03 -6.97915e-03 -9.87987e+01 The #Surf*SurfTens gives a value 568.25 bar*nm, and gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz gives a value 473.54 bar*nm. Please give me some suggestions about the inconsistency. Thanks in advance. ___ 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] surface tension calculation in g_energy
Bo Zhou wrote: Hi all, I use the option “#Surf*SurfTens” in g_engery to calculate the surface tension, but I find that I really do not know how it works after I get some inconsistent results compared with the calculation using the formula “gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz” ( there are two surfaces here and the surfaces in normal to the Z-axis). Energy Average RMSD Fluct. Drift Tot-Drift --- #Surf*SurfTen1136.52557.05 2557 0.00852598 51.1559 == ### == A V E R A G E S == ### == Pressure (bar) -1.93061e+02 -6.88599e-01 -1.66823e-02 -6.84564e-01 -1.93953e+02 -2.93803e-02 7.79006e-03 -6.97915e-03 -9.87987e+01 The “#Surf*SurfTens” gives a value 568.25 bar*nm, and “gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz” gives a value 473.54 bar*nm. Please give me some suggestions about the inconsistency. Thanks in advance. How did you calculate it? Did you divide the average pressures by the average box length? Or did you compute gamma for each step and average that (this is automatically done in the simulation and stored in the energy file). The two ways of computing are not the same. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] g_rmsf and pbc
I tried trjconv -pbc nojump to the whole protein and then calculated the rmsf of the subunits. This method seems good to some separate subunits, but other separate subunits still have strange high rmsf values. I try trjconv -pbc mol too, and i have got same results. In this simulation,the subunits are separate in the first frame. Do you have any other methods to solve this problem? On Tue, 2007-10-23 at 17:18 +0200, David van der Spoel wrote: tangxuan wrote: Mark,thanks for your reply. I am not sure what happened and I can show you the error message, Group 101 ( chK_chM) has 4070 elements Group 102 ( chM_chO) has 4070 elements Group 103 ( chO_chI) has 4070 elements Group 104 ( chJ_chL) has 4070 elements Group 105 ( chL_chN) has 4070 elements Group 106 ( chN_chP) has 4070 elements Group 107 ( chP_chJ) has 4070 elements Select a group: 22 Selected 22: 'chC' Reading frame 1 time 20001.000 Segmentation fault [miro:~/rubisco-2/chlamy_wt] % more chlamy_wt.xtc Thanks. Tang jiaowei most likely the tpr and xtc files have different number of atoms. as for your original problem, try trjconv -pbc mol in version 3.3.2 On Wed, 2007-10-24 at 00:43 +1000, Mark Abraham wrote: tangxuan wrote: Dear all, The protein I am working on is rubisco, consisting of 8 identical large subunits and 8 identical small subunits. I try to calculate RMSF for each large subunits, but the rmsf values seems much large to some large subunits. So I check the first frame of the protein structutre, and I found that these large subunits having large rmsf values seems separate in the box. Then I tried to use trjconv -pbc nojump to remove the jump for each of them in the xtc file. When I use new xtc file and original tpr file to calculate the rmsf, it shows Segmentation fault error. This may be because the coordinators of atoms in the tpr file are very diffrent from that in the fist frame. Do you know how to solve this problem? GROMACS does an inexplicable segfault almost never. It's highly likely that either there's more of an error message than you've said, or that the problem is the result some catastrophic filesystem or OS issue. Mark ___ 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 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 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] reference for urea.itp
Does anyone know the reference for the parameters for urea in the urea.itp file (found in the top directory)? Thanks, Ronen ___ 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] alpha Carbon-Aromatic ring hydrogen bond
Hi Sarbani, If I understand correctly your problem, you want to know hydrogen bond between center of the aromatic ring and CA hydrogen atom with time, you can do this in two steps (if you are not considering angle criteria). 1) first create the index files which should have two extra groups first one contain only ring carbon atoms of your aromatic residue and second one with only CA hydrogen of your interest by using make_ndx tool of GROMACS. you have to supply *.gro file to make_ndx tools and type a c1 c2 c3 c4 c5 c6 (here c1,c2,c3,c4,c5,c6 are your ring carbon atom no) a ca1 (here ca1 is your CA hydrogen atom no) then you will get new index file containing these two groups. 2) Calculate the distance between these two groups using g_dist (as mark already suggested). Hope it will help. Alok - Original Message - From: sarbani chattopadhyay To: gmx-users@gromacs.org Sent: Tuesday, October 23, 2007 3:18 PM Subject: [gmx-users] alpha Carbon-Aromatic ring hydrogen bond Hi, I want to analyze the Hydrogen bond between alpha Hydrogen and aromatic ring over the simulation time.g_hbond can't recognise this bond.is there any command by which i can do that? Sarbani -- ___ 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 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] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ?
Hello Maria, You can do it by two different methods. 1) You can increase the default VdW radii of the lipid atoms in /usr/local/gromacs/share/top/vdwradii.dat file (path might be different from your system), say 0.5 for carbon, so genbox will not add the water inside the bilayer. but you will find a gap between lipid head groups and water molecules which can be resolved after some ps dynamics. (I personally have not yet got the success ;-) ) 2) You can write a small script which can delete these water molecules, I wrote a script for the same if you need contact me offline. Hope it will help Alok - Original Message - From: maria goranovic To: gmx-users@gromacs.org Sent: Sunday, October 21, 2007 3:57 PM Subject: [gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ? Hi I am using editconf to try to add water layers on either side of my bilayer. I use the following command: genbox -cp popc.gro -box 12.47820 12.35940 10.0 -o solvated.gro -cs spc216.gro -p topology.top However, because the center of the bilayer region is less dense, a lot of water molecules are created inside the bilayer. - How does one usually edit pdb files in gromacs, in terms of, for example, removing water molecules from the center of a bilayer ? Thank you -Maria -- Maria G. Technical University of Denmark Copenhagen -- ___ 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 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] reference for urea.itp
[EMAIL PROTECTED] wrote: Does anyone know the reference for the parameters for urea in the urea.itp file (found in the top directory)? Please don't use it as is. Check literature for better models. Thanks, Ronen ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] reference for urea.itp
Thanks. I am looking at other models as well, but was wondering how the numbers in urea.itp were obtained. What type of properties they were parametrized for? Ronen -- Original message -- From: David van der Spoel [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Does anyone know the reference for the parameters for urea in the urea.itp file (found in the top directory)? Please don't use it as is. Check literature for better models. Thanks, Ronen ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 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] reference for urea.itp
[EMAIL PROTECTED] wrote: Thanks. I am looking at other models as well, but was wondering how the numbers in urea.itp were obtained. What type of properties they were parametrized for? none. just copied from the gromos 87 ff. Ronen -- Original message -- From: David van der Spoel [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Does anyone know the reference for the parameters for urea in the urea.itp file (found in the top directory)? Please don't use it as is. Check literature for better models. Thanks, Ronen ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] g_energy has no bond entry when MD analysis
Dear friends: when my MD was finished and I want to analyse the bond energy of the protein ,but g_energy did not show bond entry: the first entry is angle? When energy miniumzation finished,g_energy did show G96 bond. why? Please help me! Thank you! - 雅虎邮箱，终生伙伴！ ___ 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] g_energy has no bond entry when MD analysis
Dear friends: when my MD was finished and I want to analyse the bond energy of the protein ,but g_energy did not show bond entry: the first entry is angle? When energy miniumzation finished,g_energy did show G96 bond. why? So, when did you use bond length constraints? What effect would they have? Mark ___ 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
回复： Re: [gmx-users] g_energy has no bond entry when MD analysis
Yes, I use bond constraints! Mark Abraham [EMAIL PROTECTED] 写道： Dear friends: when my MD was finished and I want to analyse the bond energy of the protein ,but g_energy did not show bond entry: the first entry is angle? When energy miniumzation finished,g_energy did show G96 bond. why? So, when did you use bond length constraints? What effect would they have? Mark ___ gmx-users mailing list gmx-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 - 雅虎邮箱，终生伙伴！ ___ 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] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ?
You can do it by two different methods. 1) You can increase the default VdW radii of the lipid atoms in /usr/local/ gromacs/share/top/vdwradii.dat file (path might be different from your system), say 0.5 for carbon, so genbox will not add the water inside the bilayer. Cleaner method is to: cp /usr/local/gromacs/share/top/vdwradii.dat ./vdwradii.dat and then modify the local file. but you will find a gap between lipid head groups and water molecules which can be resolved after some ps dynamics. (I personally have not yet got the success ;-) ) Do I understand you to say that for you the gap does not completely dissapear in 500ps? Did you use semiisotropic coupling? Otherwise it will be more difficult for this space to fill in. It should fill in really quite quickly (500ps)... has for me. 2) You can write a small script which can delete these water molecules, I wrote a script for the same if you need contact me offline. I have previously posted such a script. It takes 10-30 minutes to run since it's not sophisticated, but it does work very well. http://www.gromacs.org/pipermail/gmx-users/2006-May/021526.html I forgot to mention that in the previously referenced script there is an assumption that you use a 3 atom water molecule. If you use tip4p then you would want if [ $count = 3 ]; then count=0 fi to be changed to: if [ $count = 4 ]; then count=0 fi and etc for tip5p. Hope it will help Alok - Original Message - Hi I am using editconf to try to add water layers on either side of my bilayer. I use the following command: genbox -cp popc.gro -box 12.47820 12.35940 10.0 -o solvated.gro -cs spc216.gro -p topology.top However, because the center of the bilayer region is less dense, a lot of water molecules are created inside the bilayer. - How does one usually edit pdb files in gromacs, in terms of, for example, removing water molecules from the center of a bilayer ? Thank you -Maria ___ 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
