Re: [gmx-users] automating analysis using shell scripting
Hi Hassan, If you have an index file with all the groups, you can use something like: #!/bin/bash groups=`grep ^\[ index.ndx | wc -l` for ((i=0; i$groups; i++)) do echo $((i++)) $i | g_dist ... done This will take groups 0 and 1, 2 and 3, etc, passing the selections to g_dist. If you want to have all unique pairwise combinations, you can use #!/bin/bash groups=`grep ^\[ index.ndx | wc -l` for ((i=0; i$((groups-1)); i++)) do for ((j=$((i+1); j$groups;j++) do echo $i $j | g_dist ... done done Do mind using the variables $i and $j in the names of the output files, to make them unique. Hope it helps, Tsjerk On Wed, Jun 30, 2010 at 3:24 AM, Hassan Shallal hshal...@pacific.edu wrote: Thanks Justin, this is just working amazingly From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Tue 6/29/2010 6:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] automating analysis using shell scripting Hassan Shallal wrote: Dear Gromacs users, This question is much more of a linux shell scripting than of Gromacs. I have several distances to measure in my produced system for which I use g_dist. I need to shell script this so I don't have to set next to the machine while measuring those distances. The problem I face is that g_dist, and others like g_rms and g_rmsf, asks for input of the number of the group with or without an index file. My question is, how can I use shell scripting to answer those questions given by g_dist, giving it the number of the groups which is usually 0 an 1 using an index file of two atoms in the system? By doing this I can write a shell script of several g_dist lines, each is concerned with a specific distance, the shell script can input the number oif the groups to be measured, and I can do another experiment or go to the gym, or even cook something for dinner until it's done, lol Has anyone of you tried doing this? Yes, see here: http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive -Justin Thanks alot Hassan Shallal University of the Pacific Stockton, California From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Sat 6/26/2010 8:39 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 74, Issue 143 lloyd riggs wrote: Dear (Justin too), Thank you for the replies. My main problem is lack of time, but I still have the end of the proteins problem as of now. I only made the comment to justin partially as a joke, because he A) answeres on averidge about 10-20 of these a day, seems too smart to be a help center, and B) Every freind I have had in the past whom ends up overdoing on the help BB (ie, CCP4, Phsics at CERN, etc...) ends up getting screwed in the end by not balancing the myself getting my things done and making connections Vs. Helping everyone else because they know so damned much about a specific topic. All of my freinds in the similar situation started off looking about as promissing, but then get ragged once they graduate, because everyone seems to want a slave loyal to themselves as a post doc, before the professorship is obtainable, etc...and end up writting video game software, hateing academia for the way it really works Vs. the way it is supposed to work in the scientific ideology we are taught at Universities and highschool. In any case, sorry to you Justin, I didn't mean to be such an ass. Apology accepted. Please don't feel like you have to save me any trouble or look out for my productivity. I only reply to email when I really care to, and my comments are intended as helpful, not picky or overly critical :) I do appreciate this follow-up, as I have received several private emails telling me I'm a useless jerk, and they really do mean it... -Justin Stephan Watkins -- 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 list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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
RE: [gmx-users] multiple time step
Hi, Our philosophy up till now is that with bond constraints and hydrogens replaced by virtual sites one can reach a time step of 4 or 5 femtoseconds. This is roughly equal to the largest time step, used for the PME mesh part, in multiple time stepping. But we then do less work on the non-bonded and bonded interactions. Therefore we think that out aproach is somewhat more efficient. But we are thinking about implementing multiple time stepping as well. I already implemented proper reversible multiple time stepping for the typical Gromos twin-range non-bonded force setup for the 4.5 release. Berk Date: Wed, 30 Jun 2010 01:41:01 -0400 From: chris.ne...@utoronto.ca To: gmx-users@gromacs.org Subject: [gmx-users] multiple time step I recall seeing something online about how gromacs developers have decided to focus on increasing the overall speed and allowing generally large timesteps (via e.g. angle constraints) vs. implementing multiple timestepping (no mailing list ref. sorry). I agree that this is not a logically exclusive decision -- PME takes 20% of the time so if they were doing it only 1/2 as often then there is the possibility of a real speedup. Nevertheless, it would need to be tested and perhaps the developers have indeed run these tests -- I've simply not seen the results. One would think, though, that PME could nearly always be done less often than, for example, bonded interactions. I agree with Erik that the work would be large, but I disagree that the benefits would be small -- although I suspect that neither of us has any data to support such claims :). Unfortunately, the bottom line is that this is free software and if you want it then you can code it. Or at the very least, you should benchmark the benefits on NAMD and then submit an enhancement bugzilla. Chris. -- original message -- The core developers have the answer for this one, but I can make an educated guess: Implementing it would mean a LOT of work and the rewards are small. The latter because most particles will have rougly the same oscillation period if one uses all-atom forcefields and turn on virtual sites and constrains the bonds, hence the point of having multiple time steps is lost. Vitaly Chaban skrev: Chris, An interesting question... BTW, is there any philosophy of gromacs developers to avoid this algorithm in the MD engine? Vitaly multiple timesteps are not possible as far as gromacs 4.0.7. NAMD can do this. -- original message -- Is it possible to carry out multiple time step molecular dynamics simulations in Gromacs 4.0. versions ? Could you please give me some information about this issue ? Thank you very much for your attention. -- 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/-- 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] ED sampling
Hi Vijaya, could it be that you mixed something up when making the .edi file? The tool make_edi reads the total number of atoms from the provided .tpr file and saves this number with the other ED sampling information to the .edi file. The ED sampling module in mdrun then compares the number of atoms from the .edi file with the .tpr file provided to mdrun - to ensure that the .edi file was produced for the same MD system. Carsten On Jun 29, 2010, at 6:57 PM, vijaya subramanian wrote: Hi I need some information about how ED sampling works when a subset of the atoms are used for covariance analysis. Basically I would like to move the system along the first eigenvector obtained from covariance analysis of the C-alpha atoms only. From the paper Toward an Exhaustive Sampling of the Configurational Spaces of two forms of the Peptide Hormone Guanylin it appears only the C-alpha atoms are used to define the essential subspace but when I use the following commands, I get an error message saying: Fatal error: Nr of atoms in edsamp26-180fit.edi (4128) does not match nr of md atoms (294206) The commands are: tpbconv -s full180.tpr -f full180.trr -extend 5 -o edsam26-180f180.tpr -e full180.edr aprun -n 60 $GROMACS_DIR/bin/mdrun -s edsam26-180f180.tpr -nosum -o edsam26-180f180.trr -x edsam26-180f180.xtc -ei edsamp26-180fit.edi -c edsam26-180f180.gro -e edsam26-180f180.edr -g edsam26-180f180.log The ED sampling method I am using is linfix not radacc. Thanks Vijaya The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. Get busy. -- 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 -- 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/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] Dimer g_rms
Dear all, I'm running my first simulation of a dimer. When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha) to get the RMSD of the whole dimer, the graph is ascending, till reaching a value of 8 A. in this case, I take a .tpr file, a .xtc file and a .ndx file of the whole dimer. However, when I run g_rmsd on Calpha, but this time, to get the RMSD of one chain (one monomer), the graph is constant with value around 1 A. and this for both chains, when taken alone. In this case, I take a .tpr file, a .xtc file and a .ndx file of the monomer. So is this an error of using g_rms? Thank you. Carla -- 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] Dimer g_rms
On Jun 30, 2010, at 10:34 AM, Carla Jamous wrote: Dear all, I'm running my first simulation of a dimer. When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha) to get the RMSD of the whole dimer, the graph is ascending, till reaching a value of 8 A. in this case, I take a .tpr file, a .xtc file and a .ndx file of the whole dimer. However, when I run g_rmsd on Calpha, but this time, to get the RMSD of one chain (one monomer), the graph is constant with value around 1 A. and this for both chains, when taken alone. In this case, I take a .tpr file, a .xtc file and a .ndx file of the monomer. So is this an error of using g_rms? Well this is not an error. Evidently your monomers are stable (rmsd~0.1nm) and you dimer is not. This might be result of either an actual deformation of the dimer or one of your monomer is crossing the periodic boundaries and thereby the rmsd is not representative. try to trjconv your trajectory using the -pbc nojump and run g_rms again. Thank you. Carla -- 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 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] -dt
Hi gromacs users I want to know what is purpose of -dt flag in most of commands? in my analysis, different values for -dt results in outcomes have not determined trend . I used this flag for g_rms as follows : if g_rms -f pr.xtc -s pr.tpr -n pr.ndx-o 5.xvg -dt 5 so : gromacs record output every 20 ps if g_rms -f pr.xtc -s pr.tpr -n pr.ndx-o 10.xvg -dt 10 so : gromacs record output every 20 ps if g_rms -f pr.xtc -s pr.tpr -n pr.ndx-o 15.xvg -dt 15 so : gromacs record output every 60 ps if g_rms -f pr.xtc -s pr.tpr -n pr.ndx-o 20.xvg -dt 20 so : gromacs record output every 20 ps if g_rms -f pr.xtc -s pr.tpr -n pr.ndx-o 25.xvg -dt 25 so : gromacs record output every 100 ps if g_rms -f pr.xtc -s pr.tpr -n pr.ndx-o 30.xvg -dt 30so : gromacs record output every 60 ps in my simulation [ 1 frame = 4 ps ] any help will highly appreciated. -- 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] g_msd and diffusion coefficent
Dear Vitaly Chaban yes. my md simulation is equilibrioum. I did simulation of protein-dna. I want to know how protein and dna close together and interact together (approach of protein to major groove of dna). thanks alot in advance. -- 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] -dt
Hi, In the mathematical sense, gromacs will only use the frames in the trajectory for which time modulus dt equals 0 (time % dt == 0). Cheers, Tsjerk On Wed, Jun 30, 2010 at 11:47 AM, XAvier Periole x.peri...@rug.nl wrote: -dt will define the frequency of analysis that a program will do. In the cases you mention (time step = 4 fs) the program is using the frames according to -dt you give and their availability in the trajectory. On Jun 30, 2010, at 11:01, leila karami karami.lei...@gmail.com wrote: Hi gromacs users I want to know what is purpose of -dt flag in most of commands? in my analysis, different values for -dt results in outcomes have not determined trend . I used this flag for g_rms as follows : if g_rms -f pr.xtc -s pr.tpr -n pr.ndx -o 5.xvg -dt 5 so : gromacs record output every 20 ps if g_rms -f pr.xtc -s pr.tpr -n pr.ndx -o 10.xvg -dt 10 so : gromacs record output every 20 ps if g_rms -f pr.xtc -s pr.tpr -n pr.ndx -o 15.xvg -dt 15 so : gromacs record output every 60 ps if g_rms -f pr.xtc -s pr.tpr -n pr.ndx -o 20.xvg -dt 20 so : gromacs record output every 20 ps if g_rms -f pr.xtc -s pr.tpr -n pr.ndx -o 25.xvg -dt 25 so : gromacs record output every 100 ps if g_rms -f pr.xtc -s pr.tpr -n pr.ndx -o 30.xvg -dt 30 so : gromacs record output every 60 ps in my simulation [ 1 frame = 4 ps ] any help will highly appreciated. -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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] question about Gromacs and Spectroscopy
Hi all, I want to reproduce some experimental data on Spectroscopy using Gromacs. I want to know is it possible? If yes, how to do that? Is there any tutorial related to that? Any help is appreciate! regards, Baofu Qiao -- 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] the job is not being distributed
Hi, I am using MPICH2 library for gromacs. Thanks and Regards Syed Tarique Moin -- 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 about Gromacs and Spectroscopy
Baofu Qiao wrote: Hi all, I want to reproduce some experimental data on Spectroscopy using Gromacs. I want to know is it possible? If yes, how to do that? Is there any tutorial related to that? Any help is appreciate! Your question is too vague to get much useful advice. The term spectroscopy can refer to a large number of techniques. I am unaware of any tutorial related to any spectroscopic technique, however, but you might get some useful advice if you ask a more specific question (i.e., what you're actually trying to do). -Justin regards, Baofu Qiao -- 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/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] Re: gmx-users Digest, Vol 74, Issue 182
Dear Vitaly Chaban yes. my md simulation is equilibrioum. I did simulation of protein-dna. I want to know how protein and dna close together and interact together (approach of protein to major groove of dna). thanks alot in advance. Dear leila, Please look towards g_rmsdist utility of the gromacs package. This seems to be better for your needs than g_msd. Good luck. Vitaly Dr. Vitaly Chaban -- 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] RE: g_msd and diffusion coefficent
Dear Vitaly Chaban yes. my md simulation is equilibrioum. I did simulation of protein-dna. I want to know how protein and dna close together and interact together (approach of protein to major groove of dna). thanks alot in advance. Dear leila, Please look towards g_rmsdist utility of the gromacs package. This seems to be better for your needs than g_msd. Good luck. Vitaly Dr. Vitaly Chaban -- 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] Dimer g_rms
XAvier Periole skrev: On Jun 30, 2010, at 10:34 AM, Carla Jamous wrote: Dear all, I'm running my first simulation of a dimer. When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha) to get the RMSD of the whole dimer, the graph is ascending, till reaching a value of 8 A. in this case, I take a .tpr file, a .xtc file and a .ndx file of the whole dimer. However, when I run g_rmsd on Calpha, but this time, to get the RMSD of one chain (one monomer), the graph is constant with value around 1 A. and this for both chains, when taken alone. In this case, I take a .tpr file, a .xtc file and a .ndx file of the monomer. So is this an error of using g_rms? Well this is not an error. Evidently your monomers are stable (rmsd~0.1nm) and you dimer is not. This might be result of either an actual deformation of the dimer or one of your monomer is crossing the periodic boundaries and thereby the rmsd is not representative. try to trjconv your trajectory using the -pbc nojump and run g_rms again. I suspect the former. If pbc crossing is the explanation, then it would show up in the analysis of one of the monomers. Erik Thank you. Carla -- 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 -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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 about Gromacs and Spectroscopy
Hi Justin, Thanks for your reply! And sorry for the vague question due to my little knowledge on the spectroscopy. What I want to reproduce is wavenumber of C-H vibrations in alkyl chains. In NMR experiments, such wavenumber is measured to be 2000-3000 cm-1, namely in the middle region of infra red. I wonder whether I can reproduce it or not? I hope this is bit of clearer! Thanks a lot! regards, Baofu Qiao Justin A. Lemkul wrote: Baofu Qiao wrote: Hi all, I want to reproduce some experimental data on Spectroscopy using Gromacs. I want to know is it possible? If yes, how to do that? Is there any tutorial related to that? Any help is appreciate! Your question is too vague to get much useful advice. The term spectroscopy can refer to a large number of techniques. I am unaware of any tutorial related to any spectroscopic technique, however, but you might get some useful advice if you ask a more specific question (i.e., what you're actually trying to do). -Justin regards, Baofu Qiao -- 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] g_rama / mult
Hi all I used [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] command for analysis of protein. gromacs give me rama.xvg as output but during calculation : Found 68 phi-psi combinations Dihedral around 9,11 not found in topology. Using mult=3 Dihedral around 11,18 not found in topology. Using mult=3 Dihedral around 20,22 not found in topology. Using mult=3 Dihedral around 22,29 not found in topology. Using mult=3 Dihedral around 33,36 not found in topology. Using mult=3 Dihedral around 40,47 not found in topology. Using mult=3 Dihedral around 51,58 not found in topology. Using mult=3 Dihedral around 62,65 not found in topology. Using mult=3 Dihedral around 301,303 not found in topology. Using mult=3 Dihedral around 303,314 not found in topology. Using mult=3 Dihedral around 318,336 not found in topology. Using mult=3 Dihedral around 340,358 not found in topology. Using mult=3 Dihedral around 360,362 not found in topology. Using mult=3 Dihedral around 362,378 not found in topology. Using mult=3 Dihedral around 382,393 not found in topology. Using mult=3 Dihedral around 397,407 not found in topology. Using mult=3 Dihedral around 411,424 not found in topology. Using mult=3 Dihedral around 428,446 not found in topology. Using mult=3 Dihedral around 450,467 not found in topology. Using mult=3 Dihedral around 471,486 not found in topology. Using mult=3 Dihedral around 490,497 not found in topology. Using mult=3 Dihedral around 509,511 not found in topology. Using mult=3 Dihedral around 523,525 not found in topology. Using mult=3 Dihedral around 529,540 not found in topology. Using mult=3 Dihedral around 544,564 not found in topology. Using mult=3 Dihedral around 568,586 not found in topology. Using mult=3 Dihedral around 590,610 not found in topology. Using mult=3 Dihedral around 614,629 not found in topology. Using mult=3 Dihedral around 633,639 not found in topology. Using mult=3 Dihedral around 643,661 not found in topology. Using mult=3 Dihedral around 665,678 not found in topology. Using mult=3 Dihedral around 682,697 not found in topology. Using mult=3 Dihedral around 701,714 not found in topology. Using mult=3 Dihedral around 718,733 not found in topology. Using mult=3 Dihedral around 737,744 not found in topology. Using mult=3 Dihedral around 748,759 not found in topology. Using mult=3 Dihedral around 763,783 not found in topology. Using mult=3 Dihedral around 787,800 not found in topology. Using mult=3 Dihedral around 804,816 not found in topology. Using mult=3 Dihedral around 820,838 not found in topology. Using mult=3 Dihedral around 842,852 not found in topology. Using mult=3 Dihedral around 856,876 not found in topology. Using mult=3 Dihedral around 880,896 not found in topology. Using mult=3 Dihedral around 900,913 not found in topology. Using mult=3 Dihedral around 917,927 not found in topology. Using mult=3 Dihedral around 931,951 not found in topology. Using mult=3 Dihedral around 955,975 not found in topology. Using mult=3 Dihedral around 979,985 not found in topology. Using mult=3 Dihedral around 989,1007 not found in topology. Using mult=3 Dihedral around 1011,1031 not found in topology. Using mult=3 Dihedral around 1035,1055 not found in topology. Using mult=3 Dihedral around 1059,1079 not found in topology. Using mult=3 Dihedral around 1083,1090 not found in topology. Using mult=3 Dihedral around 1094,1097 not found in topology. Using mult=3 Dihedral around 1109, not found in topology. Using mult=3 Dihedral around 1115,1122 not found in topology. Using mult=3 Dihedral around 1126,1133 not found in topology. Using mult=3 is this rama.xvg file true and intact? -- 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] the job is not being distributed
I think this is not a problem of Gromacs, but the cluster you are using. Try to contact with your cluster administrator, and check the administration software. Syed Tarique Moin wrote: Hi, I am using MPICH2 library for gromacs. Thanks and Regards Syed Tarique Moin -- 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] b-factor
Hi all pdb file for my protein was obtained by solution NMR. this file is as follows : ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00 ATOM 2 CA GLY A 1 -24.037 -8.099 4.448 1.00 0.00 ATOM 3 C GLY A 1 -23.580 -6.913 3.622 1.00 0.00 ATOM 4 O GLY A 1 -23.652 -6.939 2.393 1.00 0.00 ATOM 5 H1 GLY A 1 -26.109 -7.957 4.035 1.00 0.00 ATOM 6 HA2 GLY A 1 -24.067 -7.811 5.488 1.00 0.00 ATOM 7 HA3 GLY A 1 -23.324 -8.902 4.328 1.00 0.00 ATOM 8 N SER A 2 -23.111 -5.869 4.298 1.00 0.00 pdb file obtaind from g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq command is as follws : ATOM 5 CA NGL 1 20.794 51.547 38.010 1.00 272.65 ATOM 12 CA SER 2 23.444 51.157 35.390 1.00 257.41 ATOM 23 CA SER 3 25.254 48.487 33.290 1.00 189.09 ATOM 34 CA GLY 4 28.474 47.777 31.510 1.00 114.27 ATOM 41 CA SER 5 27.814 48.657 27.860 1.00 195.51 ATOM 52 CA SER 6 31.164 48.167 26.020 1.00 217.99 ATOM 63 CA GLY 7 31.934 49.987 22.770 1.00 300.70 ATOM 70 CA LYP 8 32.204 48.057 19.510 1.00 248.64 so can I compare experimental B-factor with that calculated from MD? any help will highly appreciated. -- 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] b-factor
leila karami skrev: Hi all pdb file for my protein was obtained by solution NMR. this file is as follows : ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00 ATOM 2 CA GLY A 1 -24.037 -8.099 4.448 1.00 0.00 ATOM 3 C GLY A 1 -23.580 -6.913 3.622 1.00 0.00 ATOM 4 O GLY A 1 -23.652 -6.939 2.393 1.00 0.00 ATOM 5 H1 GLY A 1 -26.109 -7.957 4.035 1.00 0.00 ATOM 6 HA2 GLY A 1 -24.067 -7.811 5.488 1.00 0.00 ATOM 7 HA3 GLY A 1 -23.324 -8.902 4.328 1.00 0.00 ATOM 8 N SER A 2 -23.111 -5.869 4.298 1.00 0.00 pdb file obtaind from g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq command is as follws : ATOM 5 CA NGL 1 20.794 51.547 38.010 1.00 272.65 ATOM 12 CA SER 2 23.444 51.157 35.390 1.00 257.41 ATOM 23 CA SER 3 25.254 48.487 33.290 1.00 189.09 ATOM 34 CA GLY 4 28.474 47.777 31.510 1.00 114.27 ATOM 41 CA SER 5 27.814 48.657 27.860 1.00 195.51 ATOM 52 CA SER 6 31.164 48.167 26.020 1.00 217.99 ATOM 63 CA GLY 7 31.934 49.987 22.770 1.00 300.70 ATOM 70 CA LYP 8 32.204 48.057 19.510 1.00 248.64 so can I compare experimental B-factor with that calculated from MD? any help will highly appreciated. I'm currently calculating b-factors too, and there may be two things that you must think about. One is, as I understand it, that the b-factor in x-ray scattering experiments is unaffected by motions in the scattering directoion, effectively reducing the observerd mds of the atoms so that B = pi^2 * 8 * msd_p, where msd_p is only the motions perpendicular to the scattering direciton. Another thing to consider is wether isotropic b-factors is suitable in your case. Erik -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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] multiple dihedrals
Hi all, I'm using ffamber99p ff in gromacs and now I have to use some additional parameters in the force field. Regarding to designation of proper dihedrals in AMBER, in some cases there are 2 or 3 dihedrals given for a specific torsion, in which parameters(e.g. angles) differ from each other and there also has been defined periodicities of -1,-2 etc. the question is how to implement such dihedrals in GROMACS, thanks very much for any instruction. bests, Amin -- 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] Re: gmx-users Digest, Vol 74, Issue 183
not found in topology. Using mult=3 Dihedral around 979,985 not found in topology. Using mult=3 Dihedral around 989,1007 not found in topology. Using mult=3 Dihedral around 1011,1031 not found in topology. Using mult=3 Dihedral around 1035,1055 not found in topology. Using mult=3 Dihedral around 1059,1079 not found in topology. Using mult=3 Dihedral around 1083,1090 not found in topology. Using mult=3 Dihedral around 1094,1097 not found in topology. Using mult=3 Dihedral around 1109, not found in topology. Using mult=3 Dihedral around 1115,1122 not found in topology. Using mult=3 Dihedral around 1126,1133 not found in topology. Using mult=3 is this rama.xvg file true and intact? -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100630/aa154dfa/attachment.html -- -- 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! End of gmx-users Digest, Vol 74, Issue 183 ** -- Gerrit Groenhof MPI biophysical chemistry Goettingen Germany http://wwwuser.gwdg.de/~ggroenh/ -- 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] Dimer g_rms
On Jun 30, 2010, at 12:47 PM, Erik Marklund wrote: XAvier Periole skrev: On Jun 30, 2010, at 10:34 AM, Carla Jamous wrote: Dear all, I'm running my first simulation of a dimer. When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha) to get the RMSD of the whole dimer, the graph is ascending, till reaching a value of 8 A. in this case, I take a .tpr file, a .xtc file and a .ndx file of the whole dimer. However, when I run g_rmsd on Calpha, but this time, to get the RMSD of one chain (one monomer), the graph is constant with value around 1 A. and this for both chains, when taken alone. In this case, I take a .tpr file, a .xtc file and a .ndx file of the monomer. So is this an error of using g_rms? Well this is not an error. Evidently your monomers are stable (rmsd~0.1nm) and you dimer is not. This might be result of either an actual deformation of the dimer or one of your monomer is crossing the periodic boundaries and thereby the rmsd is not representative. try to trjconv your trajectory using the -pbc nojump and run g_rms again. I suspect the former. If pbc crossing is the explanation, then it would show up in the analysis of one of the monomers. Not necessary! If the dimer separates across the boundaries you have a problem of fitting the two together while they are separated. This is only if you use the dimer. The monomers would be fine. The indication that it is the former comes from the rmsd that seem to increase gradually up to 0.8 nm. Erik Thank you. Carla -- 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 -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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 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] g_rama / mult
Hi Shahab, I used [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] command for analysis of Was that your actual command line? If you used a .tpr, why didn't it have all the dihedrals defined then? How did you get it? Anyway, you should be able to assert that the dihedrals mentioned are in fact your phi/psi dihedrals and should have multiplicity of 3. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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] Dimer g_rms
Hi, Not necessary! If the dimer separates across the boundaries you have a problem of fitting the two together while they are separated. This is only if you use the dimer. The monomers would be fine. That was the case before gromacs 4. But the current versions don't keep molecules whole. This means that a PBC effect will show up in at least one monomer, if there is splitting over the boundaries. It also means that the jumps due to this are much smaller, and may not be as easily identified as before. That's a general word of caution, unrelated to the issue mentioned here. Concluding, if the version is 4, the increase in RMSD may either be due to splitting or due to relative motion of the domains, but the evolution of the RMSD (sudden or gradual) will tell which is the case. Otherwise, the increase will be due to relative motion of the domains. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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] Re:Chain terminus
Dear All, I had posted here a week or so ago, but fixed my problem, and wanted to post it, and ask if somone has a better method for this: Basically, I have 5 different proteins A-E in a pdb file. I can generate a toplogy initially with pdb2gmx automated, which places the NH3 and COO- terminus. The resulting .gro file looses the chain ID's. This initial .gro and .top file works for runs (MD or EM). I then add a box and waters, and the genbox has a built in code for changing the .top file to match the water, which also keeps the terminal ends properly. These files work for runs (MD and EM) Now, then I add Ions (Na, K, Mg, Ca, Cl). The .top file however is not updated with genion. The resulting .pdb or .gro output still has no chain ID's, and there is a change in the number/type of atoms so a new .top has to be generated. If I use either of the new .gro or .pdb files, the terminal ends are not maintained, nor can pdb2gmx recognize the terminus in the interactive session without chain IDS, and the resulting .top files leed to MD and EM runs crashing, or not even initiallizing. To get around this, I write out a .pdb, cut and paste the protein portion only and add back the chain IDs, which allows interactive assignment of the terminuses. This is however time consuming, as it has to be done each time for each ion. I woundered if anyone knows how to do this more efficienttly, like the genbox or anothe way? Also, I probably would have not figured this out so fast without the replies I had, mostly. Mit freundlichen Grüsse Stephan Watkins -- GMX DSL: Internet-, Telefon- und Handy-Flat ab 19,99 EUR/mtl. Bis zu 150 EUR Startguthaben inklusive! http://portal.gmx.net/de/go/dsl -- 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] Dimer g_rms
Thank you for all your replies. Actually, I have already applied trjconv -pbc. So I'm sure that my analysis is on a whole protein, centered in my box. I'm using gromacs 4.0.3 So I think that you were right by saying that my dimer is not stable while my monomers are. But now, I have to fgure out why. Thanks again, Carla On Wed, Jun 30, 2010 at 1:54 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi, Not necessary! If the dimer separates across the boundaries you have a problem of fitting the two together while they are separated. This is only if you use the dimer. The monomers would be fine. That was the case before gromacs 4. But the current versions don't keep molecules whole. This means that a PBC effect will show up in at least one monomer, if there is splitting over the boundaries. It also means that the jumps due to this are much smaller, and may not be as easily identified as before. That's a general word of caution, unrelated to the issue mentioned here. Concluding, if the version is 4, the increase in RMSD may either be due to splitting or due to relative motion of the domains, but the evolution of the RMSD (sudden or gradual) will tell which is the case. Otherwise, the increase will be due to relative motion of the domains. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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 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] g_rama / mult
Dear Tsjerk Wassenaar thanks for your attentions. ok. [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] is my actual command line. I get tpr file by command : grompp -f *.mdp -c *.gro -p *.top -n *.ndx -o *.tpr where I should put multiplicity of 3 (what file) ? -- shahab -- 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] b-factor
On Wed, 2010-06-30 at 13:07 +0200, Erik Marklund wrote: leila karami skrev: Hi all pdb file for my protein was obtained by solution NMR. this file is as follows : ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00 ATOM 2 CA GLY A 1 -24.037 -8.099 4.448 1.00 0.00 ATOM 3 C GLY A 1 -23.580 -6.913 3.622 1.00 0.00 ATOM 4 O GLY A 1 -23.652 -6.939 2.393 1.00 0.00 ATOM 5 H1 GLY A 1 -26.109 -7.957 4.035 1.00 0.00 ATOM 6 HA2 GLY A 1 -24.067 -7.811 5.488 1.00 0.00 ATOM 7 HA3 GLY A 1 -23.324 -8.902 4.328 1.00 0.00 ATOM 8 N SER A 2 -23.111 -5.869 4.298 1.00 0.00 pdb file obtaind from g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq command is as follws : ATOM 5 CA NGL 1 20.794 51.547 38.010 1.00 272.65 ATOM 12 CA SER 2 23.444 51.157 35.390 1.00 257.41 ATOM 23 CA SER 3 25.254 48.487 33.290 1.00 189.09 ATOM 34 CA GLY 4 28.474 47.777 31.510 1.00 114.27 ATOM 41 CA SER 5 27.814 48.657 27.860 1.00 195.51 ATOM 52 CA SER 6 31.164 48.167 26.020 1.00 217.99 ATOM 63 CA GLY 7 31.934 49.987 22.770 1.00 300.70 ATOM 70 CA LYP 8 32.204 48.057 19.510 1.00 248.64 so can I compare experimental B-factor with that calculated from MD? any help will highly appreciated. I'm currently calculating b-factors too, and there may be two things that you must think about. One is, as I understand it, that the b-factor in x-ray scattering experiments is unaffected by motions in the scattering directoion, effectively reducing the observerd mds of the atoms so that B = pi^2 * 8 * msd_p, where msd_p is only the motions perpendicular to the scattering direciton. Another thing to consider is wether isotropic b-factors is suitable in your case. Erik I don't think the scattering direction is a significant factor. Each atom occurs in multiple asymmetric units, and so in multiple orientations in the crystal, depending on the spacegroup. In any case, the diffraction intensities are averaged over multiple observations, taken at different crystal orientations with respect to the beam. More serious is that the B factor soaks up many sources of uncertainty: molecular motion (e.g. from crystal phonons), internal motions, static disorder, errors in the data, effects of partial occupancy, etc. In my experience, the rmsd calculated from a B factor is much larger than that calculated from MD, and quantitative comparison is impossible. But you may well be able to see qualitative similarities. Note also that you are comparing the molecule in solution with the molecule in the crystal, and there will certainly be differences near crystal contacts. There is no B factor for NMR structures. The closest equivalent is to look at the variation between MODELs in a PDB entry. Cheers Martyn -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * *** -- 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] g_rama / mult
Hi Shahab, The dihedral definitions should be in the .top file. But you don't give any clue to what you've done or what you're doing, so there's nothing more for us to say to try and help you. ok. [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] is my actual command line. So you're actually using wild cards for these commands? That may work, but it is clearer if you use explicit file names. It may help to google 'how to ask questions the smart way' to prepare yourself for another round of free assistance. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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] residence time of water molecule
Hi how to obtain residence time of water molecule using md simulation and gromacs? What is the best way to do this? Please suggest. -- atila -- 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] the job is not being distributed
MPICH is known to have problems with GROMACS under at least some circumstances. Try OpenMPI Mark - Original Message - From: Syed Tarique Moin taris...@yahoo.com Date: Wednesday, June 30, 2010 22:36 Subject: [gmx-users] the job is not being distributed To: gmx-users@gromacs.org --- | Hi, Thanks but the with AMBER its working. If it had been the problem of cluster. It should be with AMBER too. Regards Syed Tarique Moin | --- -- 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 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] Re: gromacs with CMAP
hi, all Finally figured out that it was because all numbers in the cmap.itp file must be separated by only one space,otherwise the program will read in a zero. I would suggest this to be fixed in the release version. have a nice day. dawei On Tue, Jun 29, 2010 at 9:05 AM, Da-Wei Li lida...@gmail.com wrote: It is because I want to apply cmap to my own stuff. I can define my own 2D grid potential and apply to two sequential dihedral angles by add one line in the topol file. However, the testing result is really unexpected. dawei On Tue, Jun 29, 2010 at 8:53 AM, Per Larsson per.lars...@sbc.su.se wrote: Hi, I do not fully understand what you are trying to do, but currently CMAP is only available for the standard amino acid residues present in the rtp-file for the Charmm-forcefield, and the values for the grid are specified in the cmap.itp-file. Do you use something else? /Per 29 jun 2010 kl. 14.45 skrev Da-Wei Li: HI, David, thanks for your advise. I remove the bond angle force and get same result. It is really strange. If I set +5 on all the 24*24 grid, I just get a inverted distribution and if I set 0 on all grid, I will get a uniformed distribution. It is like that 27 regions are force to have zero cmap potential. I cannot attach figure due to size limit the list. I have sent the figure to you directly. best, dawei -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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] Re:Chain terminus
- Original Message - From: lloyd riggs lloyd.ri...@gmx.ch Date: Wednesday, June 30, 2010 21:55 Subject: [gmx-users] Re:Chain terminus To: gmx-users@gromacs.org Dear All, I had posted here a week or so ago, but fixed my problem, and wanted to post it, and ask if somone has a better method for this: Basically, I have 5 different proteins A-E in a pdb file. I can generate a toplogy initially with pdb2gmx automated, which places the NH3 and COO- terminus. The resulting .gro file looses the chain ID's. This initial .gro and .top file works for runs (MD or EM). I then add a box and waters, and the genbox has a built in code for changing the .top file to match the water, which also keeps the terminal ends properly. These files work for runs (MD and EM) Now, then I add Ions (Na, K, Mg, Ca, Cl). The .top file however is not updated with genion. The resulting .pdb or genion -p should do all this for you. I imagine decent tutorial material points this out... .gro output still has no chain ID's, and there is a change in Correct, because GROMACS doesn't care about them because it makes no post-pdb2gmx use of them. the number/type of atoms so a new .top has to be generated. If I use either of the new .gro or .pdb files, No, you only need a modified .top. It's straightforward to make sure that you have #include ions.itp and then to edit the [molecules] section. Compare your before-and-after .top files with the diff tool to see what I mean. the terminal ends are not maintained, nor can pdb2gmx recognize the terminus in the interactive session without chain IDS, and the resulting .top files leed to MD and EM runs crashing, or not even initiallizing. To get around this, I write out a .pdb, cut and paste the protein portion only and add back the chain IDs, which allows interactive assignment of the terminuses. This is however time consuming, as it has to be done each time for each ion. I woundered if anyone knows how to do this more efficienttly, like the genbox or anothe way? genion -p or a few minutes with your .top file and a text editor post-genion would have sufficed. Also, I probably would have not figured this out so fast without the replies I had, mostly. If you'd told us the problem was in producing a post-genion .top, then you might have been told about genion -p straight away. I don't think I ever understood why (you thought) you needed chain IDs - that could have been my oversight, but I certainly wasn't motivated to delve into your mind to find out why you wanted them. This is a good lesson in not presupposing the form of the answer to a problem when asking for help :-) Describe the real problem, not only your secondary problems with your solution approach. The How to ask questions the smart way website makes this advice too! 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
Re: [gmx-users] question about Gromacs and Spectroscopy
- Original Message - From: Baofu Qiao qia...@gmail.com Date: Wednesday, June 30, 2010 20:57 Subject: Re: [gmx-users] question about Gromacs and Spectroscopy To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Hi Justin, Thanks for your reply! And sorry for the vague question due to my little knowledge on the spectroscopy. What I want to reproduce is wavenumber of C-H vibrations in alkyl chains. In NMR experiments, such wavenumber is measured to be 2000-3000 cm-1, namely in the middle region of infra red. I wonder whether I can reproduce it or not? So you'll need to calculate accurate force constants of molecular vibrations of meaningful conformations. MD might be good for getting to sample a useful set of conformations, but QM on the resulting conformations will give you better estimates of force constants. It sounds like you need to spend some time reading up on this stuff. 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
[gmx-users] the job is not being distributed
Hi, Thanks a lot, i will try openmpi. Regards Syed Tarique Moin -- 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] Pull code
Hi all I am commencing the initial stages for he calculation of potential of mean force of bringing together two cage molecules. I am following the tutorial in such an exercise at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html In contrast to the tutorial I want to bring the two molecules together along the z axis. I have generated an initial configuration in which the COMs of the two molecules are 5.07 nm apart. In the tutorial to separate a substrate from a protein you use the following parameters in the mdp file. ; Pull code pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per n pull_k1 = 1000 ; kJ mol^-1 nm^- How should I alter this to pull the molecules together along the z axis? I would've thought the following but I'm not too sure pull= umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_rate1 = -0.01 pull_k1 = 1000 Obviously I have to play with the values, but it is the sign that I'm interested in. Many Thanks Gavin -- 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] Pull code
Gavin Melaugh wrote: Hi all I am commencing the initial stages for he calculation of potential of mean force of bringing together two cage molecules. I am following the tutorial in such an exercise at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html In contrast to the tutorial I want to bring the two molecules together along the z axis. I have generated an initial configuration in which the COMs of the two molecules are 5.07 nm apart. In the tutorial to separate a substrate from a protein you use the following parameters in the mdp file. ; Pull code pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per n pull_k1 = 1000 ; kJ mol^-1 nm^- How should I alter this to pull the molecules together along the z axis? I would've thought the following but I'm not too sure pull= umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_rate1 = -0.01 pull_k1 = 1000 Obviously I have to play with the values, but it is the sign that I'm interested in. Have you tried it? I think it should do what you want. Otherwise, it is probably easier to use pull_geometry = direction and specify the actual vector along which to pull. The tutorial is only really useful from a conceptual standpoint, and for a system in which pulling is applied in only one direction to cause a positive displacement. -Justin Many Thanks Gavin -- 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/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] Gromacs to APBS
Dear Gromacs users, I need to determine electric potential on each atom, and I know that APBS has such function. I wanted to first minimize the energies through gromacs and then use the apbs to do the electrostatic calculations. Can you please tell me what file do I need to convert to pqr after running energy minimization? I have read in one of the letters in the archive that editconf can turn .tpr into .pqr through -mead option, but this confused me, because mdrun does not give .tpr files as output. Should I just use -c option to get a .pdb file and the convert it to .pqr? Also, will this file contain water molecules inputed by gromacs? Will this contradict with apbs solvent? Thank you very much. Cheers, Vladimir Lankevich -- 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] Pull code
Hi Justin Thanks. If I use the pull_geometry = direction I would go for the following jus t to pull the molecules together in the z direction. pull= umbrella pull_geometry = direction pull_start = yes pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.01 pull_k1 = 1000 Does this seem reasonable? Also in the pull_rate what is meant by the 'rate of change of the reference position'? (Is it the position of the reference group, if so what if I don't want it to change?) Cheers Gavin -- 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] Pull code
Gavin Melaugh wrote: Hi Justin Thanks. If I use the pull_geometry = direction I would go for the following jus t to pull the molecules together in the z direction. pull= umbrella pull_geometry = direction pull_start = yes pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.01 pull_k1 = 1000 Does this seem reasonable? Also in the pull_rate what is meant by the Probably. Try it. 'rate of change of the reference position'? (Is it the position of the reference group, if so what if I don't want it to change?) It is the rate of change of the reference position, which is the position at the outset of the simulation. Your objective is to pull your two species together, right? I don't see why you wouldn't want it to change. You're not changing anything about pull_group0 (your reference group), since you aren't setting pull_rate0. Everything is applied to pull_group1 (hence _rate1, _k1, etc). -Justin Cheers Gavin -- 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/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] the job is not being distributed
Hello, I have successfully compiled gromacs with openmpi but i see the same problem that the jobs is still not distributed to other nodes but showing all the processor in node and it should be distributed. Thanks and regards Syed Tarique Moin -- 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] Overflow problem with test-particle insertion
Hello Gromacs users, I've been doing some simple NVT simulations of Lennard-Jones particles using the built-in 12-6 potential and a tabulated version (vdwtype=user) of this same potential. Both give practically identical results for the density and pressure, but differ in the chemical potential computed using the tpi mode in mdrun. The chemical potentials end up having the same order of magnitude, but the chemical potential for the built-in function seems to be systematically lower, e.g. 3.48 kJ/mol (built-in) vs. 6.26 kJ/mol (tabulated). The difference is smaller for the double precision version of mdrun (e.g. 7.19 kJ/mol vs. 7.55 kJ/mol). I ran some simulations in debug mode, and looked at the energies and coordinates of each insertion. It seems like 99.9% percent of the them are identical, but when the insertion energy is especially high, the simulation using the built-in function just outputs some random number, whereas the one with the table computes something around 5e18, the number to which the table plateaus as r goes to 0. Here is an example using mdrun_d (I've removed extraneous lines from the logging file): Built-in function: Insertion # Energy x y z TPI6205 2.23227e+06 0.00961 0.91659 1.56009 TPI6206 2.29990e+06 0.01536 0.84120 1.57042 TPI6207 6.44107e+07 -0.01544 0.89706 1.55119 TPI6208 2.57252e+07 -0.00345 0.85349 1.55140 TPI6209 1.65644e+07 -0.02364 0.87913 1.57432 TPI6210 6.26137e+03 0.83206 0.68462 0.46606 TPI6211 9.31542e+09 0.78445 0.71232 0.44283 TPI6212 9.63046e+11 0.80033 0.67289 0.44387 TPI6213 7.00802e+10 0.78840 0.69046 0.44094 Tabulated function: Insertion # Energy x y z TPI6205 2.23227e+06 0.00961 0.91659 1.56009 TPI6206 2.29990e+06 0.01536 0.84120 1.57042 TPI6207 6.44107e+07 -0.01544 0.89706 1.55119 TPI6208 2.57252e+07 -0.00345 0.85349 1.55140 TPI6209 1.65644e+07 -0.02364 0.87913 1.57432 TPI6210 6.01461e+18 0.83206 0.68462 0.46606 TPI6211 9.31542e+09 0.78445 0.71232 0.44283 TPI6212 9.63046e+11 0.80033 0.67289 0.44387 TPI6213 7.00802e+10 0.78840 0.69046 0.44094 Notice that for insertion #6210, the built-in function outputs 6.26137e+03. I checked the coordinates of the other particles in this frame, and there is a particle at (0.829, 0.686, 0.466), so I would think the insertion energy would be really high; hence the value of 6e18 for the tabulated function. I am using Gromacs 4.0.7 straight from the Ubuntu lucid repository ( http://packages.ubuntu.com/lucid/gromacs). I am running it on the i386 architecture. Thanks, Kevin -- 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] index groups
*I read thorough the manual on index groups and creating index file. This is the command I tried: make_ndx -f index.gro -o index.ndx * with index.gro you proposed: [ special ] 1 3 [ all ] 1 2 3 4 error I get: Reading structure file --- Program make_ndx, VERSION 4.0.7 Source code file: confio.c, line: 728 Fatal error: Invalid line in index.gro for atom 1: [ all ] --- I thought maybe the group name should be changed... but it is complaining of sth I cant figure out. Also I am asking the following Q just for the sake of learning. I dont want to do something blindly :) - can you please let me know what is the justification behind using 1 3 in first group. * *- I read about default groups. like system where all atoms are defined. So why do we need to define all group again? * Thanks, * -- 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] index groups
Moeed wrote: *I read thorough the manual on index groups and creating index file. This is the command I tried: make_ndx -f index.gro -o index.ndx * with index.gro you proposed: I posted an index file suitable for use as is. It is not a .gro file. I created the index file using a simple text editor. For a very simple 4-atom system, it is probably faster to skip make_ndx. [ special ] 1 3 [ all ] 1 2 3 4 error I get: Reading structure file --- Program make_ndx, VERSION 4.0.7 Source code file: confio.c, line: 728 Fatal error: Invalid line in index.gro for atom 1: [ all ] --- I thought maybe the group name should be changed... but it is complaining of sth I cant figure out. Also I am asking the following Q just for the sake of learning. I dont want to do something blindly :) - can you please let me know what is the justification behind using 1 3 in first group. * These two atoms form a straight line. By telling editconf to align these atoms with the x-axis, it actually does. Telling edticonf to align the whole molecule with the x-axis does not achieve what you want. For larger structures (like proteins) a principal axis is more easily utilized without a special indx group. *- I read about default groups. like system where all atoms are defined. So why do we need to define all group again? * Because I created my own index.ndx file without using make_ndx. -Justin Thanks, * -- 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/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] Using x2top to convert a gro file to a top file
I have a .gro file and I am trying to convert is to a .top file using x2top. The .gro file is as follows: Octyl Beta Glucoside 48 1OBG O1 2.840 2.397 2.515 1OBG C2 2.938 2.408 2.468 1OBG H3 2.946 2.418 2.356 1OBG C4 2.751 2.52 2.465 1OBG H5 2.725 2.530 2.361 1OBG C6 3.004 2.528 2.536 1OBG H7 3.007 2.513 2.647 1OBG C8 2.778 2.639 2.538 1OBG H9 2.765 2.632 2.650 1OBG C 10 2.926 2.657 2.503 1OBG H 11 2.938 2.681 2.394 1OBG O 12 2.702 2.747 2.486 1OBG H 13 2.739 2.827 2.525 1OBG O 14 3.136 2.551 2.488 1OBG H 15 3.181 2.465 2.486 1OBG O 16 2.973 2.766 2.581 1OBG H 17 3.068 2.771 2.566 1OBG O 18 2.610 2.480 2.539 1OBG C 19 3.000 2.275 2.513 1OBG H 20 3.019 2.276 2.623 1OBG H 21 2.931 2.190 2.487 1OBG O 22 3.123 2.263 2.443 1OBG H 23 3.156 2.174 2.460 1OBG C 24 2.487 2.516 2.452 1OBG H 25 2.491 2.627 2.440 1OBG H 26 2.491 2.467 2.351 1OBG C 27 2.364 2.472 2.530 1OBG H 28 2.367 2.518 2.632 1OBG H 29 2.366 2.361 2.543 1OBG C 30 2.239 2.515 2.457 1OBG H 31 2.238 2.626 2.445 1OBG H 32 2.238 2.471 2.354 1OBG C 33 2.115 2.470 2.532 1OBG H 34 2.116 2.513 2.636 1OBG H 35 2.115 2.359 2.542 1OBG C 36 1.989 2.515 2.461 1OBG H 37 1.988 2.626 2.452 1OBG H 38 1.988 2.473 2.357 1OBG C 39 1.865 2.469 2.535 1OBG H 40 1.866 2.509 2.639 1OBG H 41 1.865 2.357 2.543 1OBG C 42 1.739 2.514 2.465 1OBG H 43 1.739 2.626 2.457 1OBG H 44 1.738 2.474 2.360 1OBG C 45 1.615 2.468 2.537 1OBG H 46 1.613 2.509 2.642 1OBG H 47 1.612 2.357 2.543 1OBG H 48 1.608 2.410 2.453 2.0 2.0 2.0 I have tried to convert this file to a top file but this is the error message I get: Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Looking whether force field files exist Opening library file /usr/share/gromacs/top/ffoplsaa.rtp Opening library file /usr/share/gromacs/top/ffoplsaa.n2t Opening library file /usr/share/gromacs/top/ffoplsaa.n2t There are 23 name to type translations Generating bonds from distances... atom 48 Can not find forcefield for atom C-4 with 2 bonds --- Program x2top, VERSION 4.0.7 Source code file: ../../../../src/kernel/x2top.c, line: 207 Fatal error: Could only find a forcefield type for 47 out of 48 atoms --- Throwing the Baby Away With the SPC (S. Hayward) I have tried to adjust the coordinates within the gro file but it still shows the same message. Someone please give me some proper instruction in the conversion of a .gro file to a .top file. Thank you! Sincerely, Amanda M. Watkins SBC 2012 -- 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] FWSpider Tutorial
Hi I am trying to follow the tutorial listed on http://eugen.leitl.org/chem/kerrigje/pdf_files/fwspidr_tutor.pdf with the latest version of Gromacs, 4.0.7 The commands I typed were pdb2gmx ignh ff G43a1 f 1OMB.pdb o fws.gro p fws.top editconf f fws.gro d 0.7 editconf f out.gro o fws_ctr.gro center x/2 y/2 z/2 genbox cp fws_ctr.gro cs spc216.gro o fws_b4em.gro p fws.top grompp f em.mdp c fws_b4em.gro p fws.top o fws_em.tpr genion s fws_em.tpr o fws_ion.gro nname CL- nn 2 g fws_ion.log [select Group 12: SOL] pico fws.top [reduce number of SOL by two and add 2 CL- at the end of the file] mdrun s fws_em.tpr o fws_em.trr c fws_b4pr.gro g em.log e em.edr open new terminal grompp f pr.mdp c fws_b4pr.gro r fws_b4pr.gro p fws.top o fws_pr.tpr The error I kept getting was Fatal error: Number of coordinates in coordinate file (fws_b4pr.gro, 4996) does not match topology (fws.top 4992) So what additional step do I need to take (or file to re-write) in order to solve this problem? Thanks! Nayef Daher PhD Chemical Engineering University of Alberta, Canada -- 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] Using x2top to convert a gro file to a top file
Amanda Watkins wrote: I have a .gro file and I am trying to convert is to a .top file using x2top. The .gro file is as follows: Octyl Beta Glucoside 48 1OBG O1 2.840 2.397 2.515 1OBG C2 2.938 2.408 2.468 1OBG H3 2.946 2.418 2.356 1OBG C4 2.751 2.52 2.465 1OBG H5 2.725 2.530 2.361 1OBG C6 3.004 2.528 2.536 1OBG H7 3.007 2.513 2.647 1OBG C8 2.778 2.639 2.538 1OBG H9 2.765 2.632 2.650 1OBG C 10 2.926 2.657 2.503 1OBG H 11 2.938 2.681 2.394 1OBG O 12 2.702 2.747 2.486 1OBG H 13 2.739 2.827 2.525 1OBG O 14 3.136 2.551 2.488 1OBG H 15 3.181 2.465 2.486 1OBG O 16 2.973 2.766 2.581 1OBG H 17 3.068 2.771 2.566 1OBG O 18 2.610 2.480 2.539 1OBG C 19 3.000 2.275 2.513 1OBG H 20 3.019 2.276 2.623 1OBG H 21 2.931 2.190 2.487 1OBG O 22 3.123 2.263 2.443 1OBG H 23 3.156 2.174 2.460 1OBG C 24 2.487 2.516 2.452 1OBG H 25 2.491 2.627 2.440 1OBG H 26 2.491 2.467 2.351 1OBG C 27 2.364 2.472 2.530 1OBG H 28 2.367 2.518 2.632 1OBG H 29 2.366 2.361 2.543 1OBG C 30 2.239 2.515 2.457 1OBG H 31 2.238 2.626 2.445 1OBG H 32 2.238 2.471 2.354 1OBG C 33 2.115 2.470 2.532 1OBG H 34 2.116 2.513 2.636 1OBG H 35 2.115 2.359 2.542 1OBG C 36 1.989 2.515 2.461 1OBG H 37 1.988 2.626 2.452 1OBG H 38 1.988 2.473 2.357 1OBG C 39 1.865 2.469 2.535 1OBG H 40 1.866 2.509 2.639 1OBG H 41 1.865 2.357 2.543 1OBG C 42 1.739 2.514 2.465 1OBG H 43 1.739 2.626 2.457 1OBG H 44 1.738 2.474 2.360 1OBG C 45 1.615 2.468 2.537 1OBG H 46 1.613 2.509 2.642 1OBG H 47 1.612 2.357 2.543 1OBG H 48 1.608 2.410 2.453 2.0 2.0 2.0 I have tried to convert this file to a top file but this is the error message I get: Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Looking whether force field files exist Opening library file /usr/share/gromacs/top/ffoplsaa.rtp Opening library file /usr/share/gromacs/top/ffoplsaa.n2t Opening library file /usr/share/gromacs/top/ffoplsaa.n2t There are 23 name to type translations Generating bonds from distances... atom 48 Can not find forcefield for atom C-4 with 2 bonds --- Program x2top, VERSION 4.0.7 Source code file: ../../../../src/kernel/x2top.c, line: 207 Fatal error: Could only find a forcefield type for 47 out of 48 atoms --- Throwing the Baby Away With the SPC (S. Hayward) I have tried to adjust the coordinates within the gro file but it still shows the same message. Someone please give me some proper instruction in the conversion of a .gro file to a .top file. Thank you! Instead of adjusting the coordinates, you probably need to create a proper .n2t entry for this atom type. http://www.gromacs.org/Documentation/File_Formats/.n2t_File -Justin Sincerely, Amanda M. Watkins SBC 2012 -- 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/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] FWSpider Tutorial
Nayef Daher wrote: Hi I am trying to follow the tutorial listed on http://eugen.leitl.org/chem/kerrigje/pdf_files/fwspidr_tutor.pdf with the latest version of Gromacs, 4.0.7 The commands I typed were pdb2gmx –ignh –ff G43a1 –f 1OMB.pdb –o fws.gro –p fws.top editconf –f fws.gro –d 0.7 editconf –f out.gro –o fws_ctr.gro –center x/2 y/2 z/2 genbox –cp fws_ctr.gro –cs spc216.gro –o fws_b4em.gro –p fws.top grompp –f em.mdp –c fws_b4em.gro –p fws.top –o fws_em.tpr genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log [select Group 12: SOL] pico fws.top [reduce number of SOL by two and add 2 CL- at the end of the file] mdrun –s fws_em.tpr –o fws_em.trr –c fws_b4pr.gro –g em.log –e em.edr open new terminal grompp –f pr.mdp –c fws_b4pr.gro –r fws_b4pr.gro –p fws.top –o fws_pr.tpr The error I kept getting was Fatal error: Number of coordinates in coordinate file (fws_b4pr.gro, 4996) does not match topology (fws.top 4992) So what additional step do I need to take (or file to re-write) in order to solve this problem? http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology Add the -p flag to your genion command, or update the topology manually. -Justin Thanks! Nayef Daher PhD Chemical Engineering University of Alberta, Canada -- 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/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] Re: using x2top to convert a gro file to a top file
Amanda, X2TOP is a somewhat enigmatic tool. You are never sure when it why it works or refuses to generate a topology... Try to start with PDB file instead of GRO. Try to use -pbc keyword. Try to add new lines to N2T database corresponding to all atoms of your molecule. Good luck, Vitaly I have tried to convert this file to a top file but this is the error message I get: Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Looking whether force field files exist Opening library file /usr/share/gromacs/top/ffoplsaa.rtp Opening library file /usr/share/gromacs/top/ffoplsaa.n2t Opening library file /usr/share/gromacs/top/ffoplsaa.n2t There are 23 name to type translations Generating bonds from distances... atom 48 Can not find forcefield for atom C-4 with 2 bonds --- Program x2top, VERSION 4.0.7 Source code file: ../../../../src/kernel/x2top.c, line: 207 Fatal error: Could only find a forcefield type for 47 out of 48 atoms --- Throwing the Baby Away With the SPC (S. Hayward) I have tried to adjust the coordinates within the gro file but it still shows the same message. Someone please give me some proper instruction in the conversion of a .gro file to a .top file. Thank you! Sincerely, Amanda M. Watkins SBC 2012 -- 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] Re: using x2top to convert a gro file to a top file
Vitaly Chaban wrote: Amanda, X2TOP is a somewhat enigmatic tool. You are never sure when it why it works or refuses to generate a topology... Try to start with PDB file instead of GRO. Try to use -pbc keyword. Try to add new lines to N2T database corresponding to all atoms of your molecule. The -pbc option is broken in the 4.0.x series and will cause the program to hang in every case I've seen it invoked. You must use -nopbc to get the program to complete. -Justin Good luck, Vitaly I have tried to convert this file to a top file but this is the error message I get: Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Looking whether force field files exist Opening library file /usr/share/gromacs/top/ffoplsaa.rtp Opening library file /usr/share/gromacs/top/ffoplsaa.n2t Opening library file /usr/share/gromacs/top/ffoplsaa.n2t There are 23 name to type translations Generating bonds from distances... atom 48 Can not find forcefield for atom C-4 with 2 bonds --- Program x2top, VERSION 4.0.7 Source code file: ../../../../src/kernel/x2top.c, line: 207 Fatal error: Could only find a forcefield type for 47 out of 48 atoms --- Throwing the Baby Away With the SPC (S. Hayward) I have tried to adjust the coordinates within the gro file but it still shows the same message. Someone please give me some proper instruction in the conversion of a .gro file to a .top file. Thank you! Sincerely, Amanda M. Watkins SBC 2012 -- 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/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] Re: using x2top to convert a gro file to a top file
Yes, yes... I mixed them up again... One should try that option which is not default. Vitaly Chaban wrote: Amanda, X2TOP is a somewhat enigmatic tool. You are never sure when it why it works or refuses to generate a topology... Try to start with PDB file instead of GRO. Try to use -pbc keyword. Try to add new lines to N2T database corresponding to all atoms of your molecule. The -pbc option is broken in the 4.0.x series and will cause the program to hang in every case I've seen it invoked. You must use -nopbc to get the program to complete. -Justin Good luck, Vitaly I have tried to convert this file to a top file but this is the error message I get: Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Looking whether force field files exist Opening library file /usr/share/gromacs/top/ffoplsaa.rtp Opening library file /usr/share/gromacs/top/ffoplsaa.n2t Opening library file /usr/share/gromacs/top/ffoplsaa.n2t There are 23 name to type translations Generating bonds from distances... atom 48 Can not find forcefield for atom C-4 with 2 bonds --- Program x2top, VERSION 4.0.7 Source code file: ../../../../src/kernel/x2top.c, line: 207 Fatal error: Could only find a forcefield type for 47 out of 48 atoms --- Throwing the Baby Away With the SPC (S. Hayward) I have tried to adjust the coordinates within the gro file but it still shows the same message. Someone please give me some proper instruction in the conversion of a .gro file to a .top file. Thank you! Sincerely, Amanda M. Watkins SBC 2012 -- 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/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] FWSpider Tutorial
Hi Nayef, grompp –f em.mdp –c fws_b4em.gro –p fws.top –o fws_em.tpr genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log [select Group 12: SOL] pico fws.top [reduce number of SOL by two and add 2 CL- at the end of the file] This is all fine. You take the structure before em, make a run input file from it to run genion, adding some ions. You update the topology file, which seems sensible. But then, mind you that the file with the ions is fws_ion.gro. That file you should process with the edited topology to form a run input file for EM. Now look what you're doing here: mdrun –s fws_em.tpr –o fws_em.trr –c fws_b4pr.gro –g em.log –e em.edr Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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] the job is not being distributed
Hi Syed, you have to give more information for other people to be able to understand what you are doing. What is the exact sequence of commands you use to start the mdrun job? How does your OpenMPI hostfile look like, how are your nodes called, what does mdrun print on the first lines. Without that information, nobody can help you because there is no chance to tell what is possibly going wrong. Carsten On Jun 30, 2010, at 8:21 PM, Syed Tarique Moin wrote: Hello, I have successfully compiled gromacs with openmpi but i see the same problem that the jobs is still not distributed to other nodes but showing all the processor in node and it should be distributed. Thanks and regards Syed Tarique Moin -- 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 -- 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/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] FWSpider Tutorial
Hi Nayef, the next may be useful from technical point of view. if you add the option -p with topology file as an argument to given genion options you don't have to edit the topology file by hand. for example genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log -p fws.top -pname NA+ be careful to add the names of both positive and negative ion names cause for the given example there will appear 0 NA+ ions in the topology file and the names have to correspond to the force field one uses. Cheers, Peicho. - Original Message - From: Tsjerk Wassenaar tsje...@gmail.com To: jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, June 30, 2010 10:51 PM Subject: Re: [gmx-users] FWSpider Tutorial Hi Nayef, grompp –f em.mdp –c fws_b4em.gro –p fws.top –o fws_em.tpr genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log [select Group 12: SOL] pico fws.top [reduce number of SOL by two and add 2 CL- at the end of the file] This is all fine. You take the structure before em, make a run input file from it to run genion, adding some ions. You update the topology file, which seems sensible. But then, mind you that the file with the ions is fws_ion.gro. That file you should process with the edited topology to form a run input file for EM. Now look what you're doing here: mdrun –s fws_em.tpr –o fws_em.trr –c fws_b4pr.gro –g em.log –e em.edr Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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 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] Gromacs to APBS
Hi Vladimir, In [1] there is a option, called Prometheus which allows you to create pqr files from pdb file. Please, see in tools options. I would like to suggest you try to use Prometheus and tell me if it works fine. [1] http://glu.fcfrp.usp.br:8180/prometheus/ Thanks in advance, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Wed, Jun 30, 2010 at 1:39 PM, Vladimir Lankevich vladimir.lankev...@gmail.com wrote: Dear Gromacs users, I need to determine electric potential on each atom, and I know that APBS has such function. I wanted to first minimize the energies through gromacs and then use the apbs to do the electrostatic calculations. Can you please tell me what file do I need to convert to pqr after running energy minimization? I have read in one of the letters in the archive that editconf can turn .tpr into .pqr through -mead option, but this confused me, because mdrun does not give .tpr files as output. Should I just use -c option to get a .pdb file and the convert it to .pqr? Also, will this file contain water molecules inputed by gromacs? Will this contradict with apbs solvent? Thank you very much. Cheers, Vladimir Lankevich -- 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 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] Pull code
In addition to what everyone else has said, please note that pull_dim = N N Y is going to allow X and Y distance components to get as large/small as they will without any restraint. This may be what you want, but if you want a distance, but want it to be mostly in Z, then pull_dim = Y Y Y and other parameters set appropriately. Chris. -- original message -- Gavin Melaugh gmelaugh01 at qub.ac.uk Wed Jun 30 18:27:47 CEST 2010 * Previous message: [gmx-users] the job is not being distributed * Next message: [gmx-users] Pull code * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hi all I am commencing the initial stages for he calculation of potential of mean force of bringing together two cage molecules. I am following the tutorial in such an exercise at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html In contrast to the tutorial I want to bring the two molecules together along the z axis. I have generated an initial configuration in which the COMs of the two molecules are 5.07 nm apart. In the tutorial to separate a substrate from a protein you use the following parameters in the mdp file. ; Pull code pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per n pull_k1 = 1000 ; kJ mol^-1 nm^- How should I alter this to pull the molecules together along the z axis? I would've thought the following but I'm not too sure pull= umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_rate1 = -0.01 pull_k1 = 1000 Obviously I have to play with the values, but it is the sign that I'm interested in. Many Thanks Gavin -- 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] Re: gmx-users Digest, Vol 74, Issue 189
Hi Justin I manually modified the fws.top by removing two SOL and adding 2 CL- and that still didn't work. Adding -p flag gave me another type of error, stating that input/output is wrong. I entered the genion command as such genion s fws_em.tpr o fws_ion.gro -p fws.top nname CL- nn 2 g fws_ion.log Nayef Daher wrote: Hi I am trying to follow the tutorial listed on http://eugen.leitl.org/chem/kerrigje/pdf_files/fwspidr_tutor.pdf with the latest version of Gromacs, 4.0.7 The commands I typed were pdb2gmx ignh ff G43a1 f 1OMB.pdb o fws.gro p fws.top editconf f fws.gro d 0.7 editconf f out.gro o fws_ctr.gro center x/2 y/2 z/2 genbox cp fws_ctr.gro cs spc216.gro o fws_b4em.gro p fws.top grompp f em.mdp c fws_b4em.gro p fws.top o fws_em.tpr genion s fws_em.tpr o fws_ion.gro nname CL- nn 2 g fws_ion.log [select Group 12: SOL] pico fws.top [reduce number of SOL by two and add 2 CL- at the end of the file] mdrun s fws_em.tpr o fws_em.trr c fws_b4pr.gro g em.log e em.edr open new terminal grompp f pr.mdp c fws_b4pr.gro r fws_b4pr.gro p fws.top o fws_pr.tpr The error I kept getting was Fatal error: Number of coordinates in coordinate file (fws_b4pr.gro, 4996) does not match topology (fws.top 4992) So what additional step do I need to take (or file to re-write) in order to solve this problem? http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology Add the -p flag to your genion command, or update the topology manually. -Justin Thanks! Nayef Daher PhD Chemical Engineering University of Alberta, Canada -- 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/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] Capping residues
Hi, 1) What capping residues are recognized by charmm implemented on gromacs in the latest git version? I was trying to use ACE for acetyl but it is not recognized by pdb2gmx. 2) Is it possible to define caps at residues other than those at the termini? Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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] Capping residues
Sai Pooja wrote: Hi, 1) What capping residues are recognized by charmm implemented on gromacs in the latest git version? It looks like there aren't any. Check the .rtp file to be sure. I was trying to use ACE for acetyl but it is not recognized by pdb2gmx. 2) Is it possible to define caps at residues other than those at the termini? What exactly do you consider a cap? Usually a capping residue is applied only to N- and C-termini. If you're trying to make some sort of modified sidechain, then you have to look into parameterizing it yourself. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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/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] Re: gmx-users Digest, Vol 74, Issue 189
Nayef Daher wrote: Hi Justin I manually modified the fws.top by removing two SOL and adding 2 CL- and that still didn't work. Adding -p flag gave me another type of error, stating that input/output is wrong. I entered the genion command as such The actual error message is the only useful information. I suspect, however, that Tsjerk identified your problem. You're going straight from genion to mdrun, which certainly isn't correct. Read the tutorial more carefully, surely you've skipped a step. There is no need to both use -p with genion and make manual modifications. Using genion -p just saves you the trouble of potentially making mistakes, which is what I had assumed happened. -Justin genion –s fws_em.tpr –o fws_ion.gro -p fws.top –nname CL- –nn 2 –g fws_ion.log Nayef Daher wrote: Hi I am trying to follow the tutorial listed on http://eugen.leitl.org/chem/kerrigje/pdf_files/fwspidr_tutor.pdf with the latest version of Gromacs, 4.0.7 The commands I typed were pdb2gmx –ignh –ff G43a1 –f 1OMB.pdb –o fws.gro –p fws.top editconf –f fws.gro –d 0.7 editconf –f out.gro –o fws_ctr.gro –center x/2 y/2 z/2 genbox –cp fws_ctr.gro –cs spc216.gro –o fws_b4em.gro –p fws.top grompp –f em.mdp –c fws_b4em.gro –p fws.top –o fws_em.tpr genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log [select Group 12: SOL] pico fws.top [reduce number of SOL by two and add 2 CL- at the end of the file] mdrun –s fws_em.tpr –o fws_em.trr –c fws_b4pr.gro –g em.log –e em.edr open new terminal grompp –f pr.mdp –c fws_b4pr.gro –r fws_b4pr.gro –p fws.top –o fws_pr.tpr The error I kept getting was Fatal error: Number of coordinates in coordinate file (fws_b4pr.gro, 4996) does not match topology (fws.top 4992) So what additional step do I need to take (or file to re-write) in order to solve this problem? http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology Add the -p flag to your genion command, or update the topology manually. -Justin Thanks! Nayef Daher PhD Chemical Engineering University of Alberta, Canada -- 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 -- 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/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] Gromacs to APBS
- Original Message - From: Vladimir Lankevich vladimir.lankev...@gmail.com Date: Thursday, July 1, 2010 2:39 Subject: [gmx-users] Gromacs to APBS To: gmx-users@gromacs.org Dear Gromacs users, I need to determine electric potential on each atom, and I know that APBS has such function. I wanted to first minimize the energies through gromacs and then use the apbs to do the electrostatic calculations. Can you please tell me what file do I need to convert to pqr after running energy minimization? I have read in one of the letters in the archive that editconf can turn .tpr into .pqr through -mead option, but this confused me, because mdrun does not give .tpr files as output. Should I just use -c option to get a .pdb file and the convert it to .pqr? Probably Also, will this file contain water molecules inputed by gromacs? Yes. Will this contradict with apbs solvent? Thank you very much. Probably. You can strip these with trjconv -f in.pdb -o out.pdb 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
Re: [gmx-users] the job is not being distributed
- Original Message - From: Syed Tarique Moin taris...@yahoo.com Date: Thursday, July 1, 2010 4:22 Subject: [gmx-users] the job is not being distributed To: gmx-users@gromacs.org --- | Hello, I have successfully compiled gromacs with openmpi but i see the same problem that the jobs is still not distributed to other nodes but showing all the processor in node and it should be distributed. | --- We can't help you without you providing a lot more detail. Be sure that you can run other parallel programs and have followed the MPI installation instructions on the GROMACS website. 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
Re: [gmx-users] Capping residues
- Original Message - From: Justin A. Lemkul jalem...@vt.edu Date: Thursday, July 1, 2010 9:58 Subject: Re: [gmx-users] Capping residues To: Discussion list for GROMACS users gmx-users@gromacs.org Sai Pooja wrote: Hi, 1) What capping residues are recognized by charmm implemented on gromacs in the latest git version? It looks like there aren't any. Check the .rtp file to be sure. There aren't. I had a discussion with Par Bjelkmar a while back about including some, but I don't recall the outcome. Mark I was trying to use ACE for acetyl but it is not recognized by pdb2gmx. 2) Is it possible to define caps at residues other than those at the termini? What exactly do you consider a cap? Usually a capping residue is applied only to N- and C-termini. If you're trying to make some sort of modified sidechain, then you have to look into parameterizing it yourself. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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/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 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] amber/charmm force field and HB lifetime at low temperature
Hi gromacs users: Using amber/charmm force field we simulated a solvated protein system at different temperature(300,250 and 200K). I used TIP5P water model and applied NVT ensemble . We analyzed the hydrogen bond life time correlation function(HBCF) to study the protein water interactions. At 300K, the result looks good and comparable with the literature data. But at 250 and 200K, during the initial 0-2ps, HBCF decay is very fast before it start to relax. This problem does not arise when i tried with other force field which came along with gromacs package(like GROMOS,OPLS..) I don't know where i am making mistakes; patching the amber and charmm force fields to gromacs package lead to this problem? Can anybody help me? thank you. My mdp options are: cpp = /lib/cpp constraints = hbonds constraint_algorithm = shake integrator = md dt = 0.001 ; nsteps = 50 ; nstcomm= 1; nstlist= 10 ns_type= grid nstenergy = 5; nstlog = 5; nstvout= 5; nstxout= 5; ;nstxtcout = 5; ;xtc-precision = 100 nstfout= 0 coulombtype= shift fourierspacing = 0.12 pme_order = 4 vdwtype= switch rvdw = 1.0 rlist = 1.2 rcoulomb = 1.0 pbc= xyz ;Berendsen temperature coupling is on Tcoupl = nose-hoover ; temperature bath (yes, no) tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 200 200 ;Berendsen Pressure coupling is on pcoupl = no ; pressure bath (yes, no) ;Generate velocities is on at 200 gen_vel = no ; generate initial velocities ;gen_temp= 200.0 ; initial temperature ;gen_seed= 173529; random seed ; regards, Rama -- 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] protein stability as a dimer
Hello All, I have done simulation for 1ns on a protein dimer using GROMOS96 43a1 force field. I want to study if the protein is stable as a dimer or not, so can you please give me some suggestion as to what analysis I could do for the same. I checked g_rms after the simulation, graph which I am getting is like, first rmsd is increases rapidly to 0.2nm for for 0.1 ns and then till 0.8 ns it still increased to 0.3 nm and still there are more fluctuations but and it decreses again to 0.28 nm at 0.1 ns. So what could i infer about the stability of the protein as a dimer from this data. Thanks in advance. Regards -- Sonali Dhindwal -- 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
