[gmx-users] how to increase the number of
Thanks to all that answered. I solved the problem with the approach Mark suggested and it seems to be working fine! Thanks Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ ___ 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] how to increase the number of
Dear All, I am using GROMACS 3.3.1 and i setup a simulation to run in 2 nodes of a workstation. It is running OK however now i have two extra nodes available to use in the same box and i would like to speed up the sim by using them. Is there any way to increase the number of nodes under use ? I tried tpbconv to extend the sim and increase the np vaue but it did not worked. Thanks Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ ___ 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] How to calculate the angle between side chains and helical axis
Dear All, I have performed a MD simulation of a helical peptide in a solvent box. Now I am interested on determining the angle between the helix axis and the side chain of some residues (defined by the vector form Cb to the terminal heavy atom of each residue). I am trying to do so using g_bundle... is this a good aproach? My problem with g_bundle is that I can define the top and bottom of the helix axis, but how can I define the other axis for each residue? Thanks! Cheers Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] problem regarding do_dssp
I got an error similar to that Have you correctly set the environment variable dssp pointing to the dssp executable? fro example: setenv DSSP /opt/dssp/bin/dssp Cheers Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Re: RMSD of the same protein in different solvent boxes
Thanks it worked! I useed trjconv to create a new .xtc just with the backbone and now I can do a g_rms for both simulations. Cheers Afonso Today's Topics: 1. Re: RMSD of the same protein in different solvent boxes (Tsjerk Wassenaar) 2. Re: RMSD of the same protein in different solvent boxes (Florian Haberl) 3. Re: RMSD of the same protein in different solvent boxes (Ran Friedman) -- Message: 1 Date: Mon, 5 Feb 2007 11:22:23 +0100 From: "Tsjerk Wassenaar" Subject: Re: [gmx-users] RMSD of the same protein in different solvent boxes To: "Discussion list for GROMACS users" Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Afonso, Try to first extract the protein from both simulations using trjconv, or even the backbone trajectories. Cheers, Tsjerk On 2/5/07, Afonso Duarte wrote: > Hi to All, > > I have some simulations of the same protein in different solvents, with > different number of atoms for each (different solvent number of atoms). > I would like to calculate a rmsd matrix to compar the backbone of the > different sims. > > I have tried g_rms with the -f2 option to include the second trajectory, > however it finishes with a fatal error because teh number of total atoms is > different in both trajectories. > > Does anybody know how to solve this question? Is it possible to produce the > rmsd matrix in a different way? > > Thanks in advance > > Afonso > > > __ > Fale com seus amigos de graça com o novo Yahoo! Messenger > http://br.messenger.yahoo.com/ > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -- Message: 2 Date: Mon, 5 Feb 2007 11:31:27 +0100 From: Florian Haberl Subject: Re: [gmx-users] RMSD of the same protein in different solvent boxes To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="utf-8" hi, On Monday, 5. February 2007 11:13, Afonso Duarte wrote: > Hi to All, > > I have some simulations of the same protein in different solvents, with > different number of atoms for each (different solvent number of atoms). I > would like to calculate a rmsd matrix to compar the backbone of the > different sims. > > I have tried g_rms with the -f2 option to include the second trajectory, > however it finishes with a fatal error because teh number of total atoms is > different in both trajectories. > > Does anybody know how to solve this question? Is it possible to produce the > rmsd matrix in a different way? reduce both simulations to matching atomsize, e.g. for both simulations: make_ndx (only backbone atoms) trjconv .. g_rms > > Thanks in advance > > Afonso > > __ > Fale com seus amigos de graça com o novo Yahoo! Messenger > http://br.messenger.yahoo.com/ greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) â 9131 â 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- -- Message: 3 Date: Mon, 05 Feb 2007 11:22:55 +0100 From: Ran Friedman Subject: Re: [gmx-users] RMSD of the same protein in different solvent boxes To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi, If it's the same protein you can extract the trajectories with the coordinates of the protein only using trjconv. Ran. Afonso Duarte wrote: > Hi to All, > > I have some simulations of the same protein in different solvents, > with different number of atoms for each (different solvent number of > atoms). > I would like to calculate a rmsd matrix to compar the backbone of the > different sims. > > I have tried g_rms with the -f2 option to include the second > trajectory, however it finishes with a fatal error because teh number > of total atoms is different in both
[gmx-users] RMSD of the same protein in different solvent boxes
Hi to All, I have some simulations of the same protein in different solvents, with different number of atoms for each (different solvent number of atoms). I would like to calculate a rmsd matrix to compar the backbone of the different sims. I have tried g_rms with the -f2 option to include the second trajectory, however it finishes with a fatal error because teh number of total atoms is different in both trajectories. Does anybody know how to solve this question? Is it possible to produce the rmsd matrix in a different way? Thanks in advance Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Problem running do_dssp
Dear All, I am running Gromacs 3.3.1 and I have recently installed dssp to run the do_dssp command. I have set the path correctly and the dssp seems to work ok by it self, however when i run do_dssp I get the following message: There are 25 residues in your selected group Opening library file /home/duartea/gromacs/share/gromacs/top/ss.map trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Back Off! I just backed up ddlNDmaL to ./#ddlNDmaL.1# The processor is working at 100% but no xpm or xvg files are produced... and thereading frame does not change either... Does anybody telm if i am doing something wrong? Thanks! Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Info on g_sas DGsolv
Dear All I have one question regarding the output of g_sas. In the area.xvg file that includes the hydrophobic,hydrophilic and total solvent accessible surface, also includeas a DGsolv output. I tried to find what is kind of energy (is it the total solvatation energy?) and what are the units (I am assuming kJ/mol) but I did not found it. Could somebody ellucidate me? Thanks! Cheers Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] question regarding g_sham
Hi to All, I want to use the g_sham command to have the entropy and enthalpy plots of a simulation of a protein in water. I have tried to use the EPot, EKin, and Efree, among others, as input in the graph.xvg file, toghether with the -lsh and -lss options, however the enthalpy.xpm and the entropy.xpm files are not created. Is my input correct? what kind of graph.xvg should I use for input to get the correct output. I am using version 3.3.1. Thanks Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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_sdf function in a 2D map
Hi to All! I am using the g_sdf and g_rdf functions to analyse the solvation of some molecules. With g_sdf I get nice 3D maps that describe the g_rdf ... however I would like to know how is it possible to produce 2D maps from these files (with contour lines for example). I am using Chimera to visualize the plt files however I think this software does not produce 2D from 3D surfaces. Thanks!! Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Info on the "Ellipticity at 222 nm" provided by g_helix
Dear All, I am a newbie using GROMACS and I am just going throu my first sims. I have one question regarding the output of g_helix. Using this command get a value for the "Ellipticity at 222 nm according to Hirst and Brooks" however this value is in nm (per time frame) and for 100% a-helices it shows positive values (instead of the typical negative values. I have read the paper from Hirst and Brooks, however I don understant how can one correlate the values from GROMACS with experimental ellipticity (values in mdeg and more negative when the helical content increases) PS: I found a similar question in this newsletter, however there was no reply... Thanks Afonso Abra sua conta no Yahoo! Mail - 1GB de espaço, alertas de e-mail no celular e anti-spam realmente eficaz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
