[gmx-users] g_analyze -ee
Dear all I used g_analyze -f dist.xvg -ee In the one of the my output files, I encountered Read 1 sets of 1252 points, dt = 0.0119951 std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 7.918456e+00 2.788148e+00 7.882919e-02 -0.717 -0.202 Back Off! I just backed up e11grey.xvg to ./#e11grey.xvg.2# Warning: tau2 is longer than the length of the data (15.0059) the statistics might be bad invalid fit: e.e. nan a 2.07331 tau1 3.99138 tau2 183052 Will fix tau2 at the total time: 15.0059 a fitted parameter is negative invalid fit: e.e. nan a 16.5523 tau1 10.8852 tau2 15.0059 Will use a single exponential fit for set 1 Set 1: err.est. 1.26673 a 1 tau1 1.54994 tau2 0 how to fix that? Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] trjconv in martini
Hi Sara, Please find the script as attachment. When saved, you have to make it executable using chmod +x xtcrev.py Then it should work... Cheers, Tsjerk On Sat, Dec 31, 2011 at 5:59 AM, mohammad agha mra...@yahoo.com wrote: Hi Tsjerk, Thank you for your reply, yes it is #!/usr/bin/env python May I ask you to help me? Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, December 30, 2011 8:06 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, Make sure the first line of the script is: #!/usr/bin/env python Cheers, Tsjerk On Dec 30, 2011 1:25 PM, mohammad agha mra...@yahoo.com wrote: - Forwarded Message - From: mohammad agha mra...@yahoo.com To: Tsjerk Wassenaar tsjerkw@... -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands #!/usr/bin/env python # Reverse an XTC trajectory # # (c)2011 Tsjerk A. Wassenaar # University of Groningen # from struct import unpack import sys import os def i(x): return sum([ord(x[j])(24-j*8) for j in range(4)]) def strseek(stream,s,bufsize=1): v = len(s) x = stream.read(bufsize) n = 0 while len(x) = v: m = x.find(s) if m -1: # If we found the tag, the position is the total length # read plus the index at which the tag was found n += m yield n # Now we strip the part up to and including the tag x = x[m+v:] n += v elif len(x) v: # If the tag was not found, strip the string, keeping only # the last v-1 characters, as these could combine with the # next part to be read in. # n is incremented with the number of characters taken from # the current string x (len(x)-v+1) n += len(x)-v+1 x = x[1-v:] if len(x) = v: x += stream.read(bufsize) # Get the tag to identify the start of a frame f = open(sys.argv[1]) tag = f.read(8) # Tag: magic number and number of atoms n = 92 + i(f.read(84)[-4:]) # Size of frame in bytes f.close() # Find all positions at which the tag is found and the frame lengths frames = [ i for i in strseek(open(sys.argv[1]),tag) ] nf = len(frames) lengths = [ j-i for i,j in zip(frames,frames[1:]+[nf]) ] # Reverse the lists frames.reverse() lengths.reverse() # Write the frames in reversed order f = open(sys.argv[1]) o = open(sys.argv[2],w) for pos,bytes in zip(frames,lengths): f.seek(pos) o.write(f.read(bytes)) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] trjconv in martini
Hi Tsjerk, Thanks for your reply, yas, I did this too! Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 31, 2011 11:42 AM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, Please find the script as attachment. When saved, you have to make it executable using chmod +x xtcrev.py Then it should work... Cheers, Tsjerk On Sat, Dec 31, 2011 at 5:59 AM, mohammad agha mra...@yahoo.com wrote: Hi Tsjerk, Thank you for your reply, yes it is #!/usr/bin/env python May I ask you to help me? Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, December 30, 2011 8:06 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, Make sure the first line of the script is: #!/usr/bin/env python Cheers, Tsjerk On Dec 30, 2011 1:25 PM, mohammad agha mra...@yahoo.com wrote: - Forwarded Message - From: mohammad agha mra...@yahoo.com To: Tsjerk Wassenaar tsjerkw@... -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] trjconv in martini
Hi Tsjerk, Thanks for your reply, yes, I did this, too! but my problem wasn't solved! Best RegardsSara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 31, 2011 11:42 AM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, Please find the script as attachment. When saved, you have to make it executable using chmod +x xtcrev.py Then it should work... Cheers, Tsjerk On Sat, Dec 31, 2011 at 5:59 AM, mohammad agha mra...@yahoo.com wrote: Hi Tsjerk, Thank you for your reply, yes it is #!/usr/bin/env python May I ask you to help me? Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, December 30, 2011 8:06 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, Make sure the first line of the script is: #!/usr/bin/env python Cheers, Tsjerk On Dec 30, 2011 1:25 PM, mohammad agha mra...@yahoo.com wrote: - Forwarded Message - From: mohammad agha mra...@yahoo.com To: Tsjerk Wassenaar tsjerkw@... -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] trjconv in martini
Hi Sara, You do have python installed, don't you? Maybe you have to have version 2.5 or 2.6 for this to work, although I think it's not using any features that were not already in 2.3 or 2.4. Can you post the workflow you're trying now, pasting the exact commands you use? Cheers, Tsjerk On Sat, Dec 31, 2011 at 10:29 AM, mohammad agha mra...@yahoo.com wrote: Hi Tsjerk, Thanks for your reply, yes, I did this, too! but my problem wasn't solved! Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 31, 2011 11:42 AM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, Please find the script as attachment. When saved, you have to make it executable using chmod +x xtcrev.py Then it should work... Cheers, Tsjerk On Sat, Dec 31, 2011 at 5:59 AM, mohammad agha mra...@yahoo.com wrote: Hi Tsjerk, Thank you for your reply, yes it is #!/usr/bin/env python May I ask you to help me? Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, December 30, 2011 8:06 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, Make sure the first line of the script is: #!/usr/bin/env python Cheers, Tsjerk On Dec 30, 2011 1:25 PM, mohammad agha mra...@yahoo.com wrote: - Forwarded Message - From: mohammad agha mra...@yahoo.com To: Tsjerk Wassenaar tsjerkw@... -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] trjconv in martini
Hi Tsjerk, Thank you very much from your reply, I think you're right, my problem is about python installation, I take error when I want to install python 2.5 and 2.6, now I am installing the python 2.3. My workflow is according to what you said me means: # Get a clustered reference frame trjconv -s md.tpr -f md.trr -o cluster.gro -pbc cluster -dump 20 # Extract the first part of the trajectory trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 1 # Reverse it ./xtcrev.py 1a.xtc 1a-rev.xtc and it wasn't ran here, after installation of python I will practice again your workflow. I hope work this time. I thank you very very much again. Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 31, 2011 2:18 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, You do have python installed, don't you? Maybe you have to have version 2.5 or 2.6 for this to work, although I think it's not using any features that were not already in 2.3 or 2.4. Can you post the workflow you're trying now, pasting the exact commands you use? Cheers, Tsjerk On Sat, Dec 31, 2011 at 10:29 AM, mohammad agha mra...@yahoo.com wrote: Hi Tsjerk, Thanks for your reply, yes, I did this, too! but my problem wasn't solved! Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 31, 2011 11:42 AM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, Please find the script as attachment. When saved, you have to make it executable using chmod +x xtcrev.py Then it should work... Cheers, Tsjerk On Sat, Dec 31, 2011 at 5:59 AM, mohammad agha mra...@yahoo.com wrote: Hi Tsjerk, Thank you for your reply, yes it is #!/usr/bin/env python May I ask you to help me? Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, December 30, 2011 8:06 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, Make sure the first line of the script is: #!/usr/bin/env python Cheers, Tsjerk On Dec 30, 2011 1:25 PM, mohammad agha mra...@yahoo.com wrote: - Forwarded Message - From: mohammad agha mra...@yahoo.com To: Tsjerk Wassenaar tsjerkw@... -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] trjconv in martini
Hi Sara, # Extract the first part of the trajectory trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 1 That should be -e 19 :) But you can also use -e 20. Probably that is better. I first thought it'd be better to avoid a double frame, but since trjcat is used to combine the parts again, it doesn't matter. Good luck, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] trjconv in martini
Hi Tsjerk, Thank you very much from your help. Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 31, 2011 3:41 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, # Extract the first part of the trajectory trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 1 That should be -e 19 :) But you can also use -e 20. Probably that is better. I first thought it'd be better to avoid a double frame, but since trjcat is used to combine the parts again, it doesn't matter. Good luck, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] After installation help
Hello buddies, I'm a very beginner in gromacs and I just got a trick but simple situation (for you :D). After the installation of my gromacs on ubuntu 11.10 I opened the .bashrc file and put the following code in the following place as instructed by installation session on the webpage: .BASHRC file # Add an alert alias for long running commands. Use like so: # sleep 10; alert alias alert='notify-send --urgency=low -i $([ $? = 0 ] echo terminal || echo error) $(history|tail -n1|sed -e '\''s/^\s*[0-9]\+\s*//;s/[;|]\s*alert$//'\'')' # Alias definitions. # You may want to put all your additions into a separate file like # ~/.bash_aliases, instead of adding them here directly. # See /usr/share/doc/bash-doc/examples in the bash-doc package. if [ -f ~/.bash_aliases ]; then . ~/.bash_aliases fi #this should be an access to gromacs source . /usr/local/gromacs/bin/GMXRC # enable programmable completion features (you don't need to enable # this, if it's already enabled in /etc/bash.bashrc and /etc/profile # sources /etc/bash.bashrc). if [ -f /etc/bash_completion ] ! shopt -oq posix; then . /etc/bash_completion fi I already tried using . /usr/local/gromacs/GMXRC in the begin and also just /usr/local/gromacs/GMXRC (without the point) and even thereafter I couldn't run the program. Unfortunately I really don't know what to do I've already read the final installation instructions many times and tried to google something related but I had no luck. Please someone can provide me some light on this issue?? Thanks all of you. Willian Felix -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Configurations stored in REMD trajectories
Thanks :D 2011/12/30 Mark Abraham mark.abra...@anu.edu.au On 31/12/2011 7:03 AM, César Ávila wrote: Dear all, perhaps someone can help me with this doubt. When a REMD simulation is run, which configuration is stored for any given replica, the one before the exchange or the one that we get after the exchange (i.e. the exchange partner configuration)? Replica exchange occurs after all output - it's essentially the last thing that happens in the main loop. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: cnt topology
I hope you understand that I canNOT fix the problem by just looking at several thousands on numbers in your topology... My preliminary guess would be that the problem is localized in the dihedral section, i.e. you don't define all the necessary dihedrals or define some of them inconsistently with your GRO file. I would start with visualizing you GRO including atom numbers and checking manually if all the dihedrals you actually see are present in the topology file. Usually, considering the very first circle of the carbon atoms will give your an answer. There is also a lazy solution. If you don't need a flexible tube, you can just freeze its carbon atoms (in the MDP file), so that the geomerty will be stable at all times -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA On Sat, Dec 31, 2011 at 1:42 PM, Zahra M s_zahra_mous...@yahoo.com wrote: sorry I forget to attach my cnt topology file From: Dr. Vitaly V. Chaban vvcha...@gmail.com To: Zahra M s_zahra_mous...@yahoo.com Cc: gmx-users@gromacs.org Sent: Saturday, December 31, 2011 8:51 PM Subject: Re: Zahra: I believe the problem is in your topology (*.TOP) file which you don't attach. From your pictures, we see that the system does not survive energy minimization, so the intramolecular interactions are not simulated wisely. Happy New Year, Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA On Sat, Dec 31, 2011 at 11:58 AM, Zahra M s_zahra_mous...@yahoo.com wrote: Hi dear Dr. Vitaly I'm simulating a system containing CNT and a protein with GROMACS, and I encounter with some problems, as I understood (by reading articles) you've worked on CNT simulation alot, so I decided to ask you for help. I wish you help me to solve my problem. As I mentioned my system contains CNT and protein, in a dodecahedron unit cell. when I run EM (although in vacuum) the shape of CNT changes, and its bonds crash. here are my MD parameters for EM: integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) domain-decomposition = no coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) fourierspacing = 0.20 but when I run mdrun command these lines appear in terminal: There were 16 inconsistent shifts. Check your topology ... There were 16 inconsistent shifts. Check your topology Warning: 1-4 interaction between 418 and 533 at distance 2.620 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size There were 16 inconsistent shifts. Check your topology 2.27716e+06, atom= 536 Step= 1, Dmax= 1.0e-02 nm, Epot= 2.74550e+07 Fmax= 2.26527e+06, atom= 536 There were 16 inconsistent shifts. Check your topology Step= 2, Dmax= 1.2e-02 nm, Epot= 2.71314e+07 Fmax= 2.25101e+06, atom= 536 There were 16 inconsistent shifts. Check your topology Step= 3, Dmax= 1.4e-02 nm, Epot= 2.67459e+07 Fmax= 2.23390e+06, atom= 536 There were 16 inconsistent shifts. Check your topology Step= 4, Dmax= 1.7e-02 nm, Epot= 2.62873e+07 Fmax= 2.21339e+06, atom= 536 There were 16 inconsistent shifts. Check your topology Step= 5, Dmax= 2.1e-02 nm, Epot= 2.57427e+07 Fmax= 2.18879e+06, atom= 536 There were 16 inconsistent shifts. Check your topology Step= 6, Dmax= 2.5e-02 nm, Epot= 2.50973e+07 Fmax= 2.15928e+06, atom= 536 There were 16 inconsistent shifts. Check your topology Step= 7, Dmax= 3.0e-02 nm, Epot= 2.43348e+07 Fmax= 2.12391e+06, atom= 536 There were 16 inconsistent shifts. Check your topology Step= 8, Dmax= 3.6e-02 nm, Epot= 2.34369e+07 Fmax= 2.08150e+06, atom= 536 There were 16 inconsistent shifts. Check your topology Step= 9, Dmax= 4.3e-02 nm, Epot= 2.23854e+07 Fmax= 2.03066e+06, atom= 536 There were 16 inconsistent shifts. Check your topology Step= 10, Dmax= 5.2e-02 nm, Epot= 2.11653e+07 Fmax= 1.96974e+06, atom= 536 There were 16 inconsistent shifts. Check your topology
[gmx-users] detective work before or after creating a topology?
Hello I have two questions. First question: If you parameterize a force field (which means that you make changes in atomtypes.atp, create a new .rtp and a .hdb file, make changes in ffnonbonded.itp, create a residuetypes.dat file and finally make symbolic links to gromacs) and you use pdb2gmx to get a topology file (topol.top) and this file has not all informations or something is wrong what is better: 1.) Try to fix missing or false information in the topology file (detective work in the topology) or should one 2.) Try to fix something in the created and modified files of the force field and parametrization Second question: This question is implied in someway: If everything in the parametrization is correct will be the topology you get by pdb2gmx alway correct for further calculations? To summarize: If someone has bad (even false) topology, should you try to fix the topology or is a bad topology always a strong identification for bad parametrization? Thanks Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] detective work before or after creating a topology?
On 1/01/2012 7:45 AM, Lara Bunte wrote: Hello I have two questions. First question: If you parameterize a force field (which means that you make changes in atomtypes.atp, create a new .rtp and a .hdb file, make changes in ffnonbonded.itp, create a residuetypes.dat file and finally make symbolic links to gromacs) and you use pdb2gmx to get a topology file (topol.top) and this file has not all informations or something is wrong what is better: 1.) Try to fix missing or false information in the topology file (detective work in the topology) or should one 2.) Try to fix something in the created and modified files of the force field and parametrization If you have done a complete parameterization and constructed a complete way for pdb2gmx to built a topology from a coordinate file then the problem cannot arise. If you haven't done the former, then go back and do it. If you haven't done the latter, then it is probably right to fix the contents of the force field directory (rather than the produced topology) on the theory that you may want to use the force field again some time. Second question: This question is implied in someway: If everything in the parametrization is correct will be the topology you get by pdb2gmx alway correct for further calculations? To summarize: If someone has bad (even false) topology, should you try to fix the topology or is a bad topology always a strong identification for bad parametrization? They're orthogonal. The topology expresses a particular combination of the parameters that implements a model. Both topology and parameters have to be right for the model to work, and failure doesn't localize the problem to one or the other aspect. Just as with writing, even if the parser (grompp) thinks the words you are using make grammatical sense (no error, so sufficient parameter values and connectivity), only you can judge whether the way in which you have followed the rules should make for a meaningful sentence (valid model). 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Obtain the flux of water
Dear all, Whether there is a program in Gromacs that would directly or indirectly obtained the flux of water ? How to obtain the flux water in Gromacs ? Best Regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Hi, May I ask you a question about the free energy calculation tutorial?
yywang wrote: At 2011-12-31 04:42:12,Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: yywang wrote: Dear Justin Lemkul, I find a tutorial about the free energy calculation by g_bar in Gromacs. ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html) I have a question when I use this tutorail. That is I cannot use muti-cores in cluster. When I try to use mpirun -np 2 or more, an error occured (There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 6.46036 nm 228 Change the number of nodes or mdrun option -rdd) But when i turn the mpirun off ,eg mpirun -np 1 mdrun -nt 2 , everything is OK. I do not know the basis for why MPI vs. threading would lead to different behavior. I use threading by default on a dual-core machine since the tutorial system is small. Since my model is a little big, the speed of use 1 core and 2 threads is too slow, is there any method to change this situation, or do you know any paramater that control this? Are we still talking about the tutorial system? It is quite small. The DD cell size you've posted above seems to be from a different system. I cannot offer personalized advice for individual systems that I've not worked with. The best information is online: http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm -Justin Sorry I haven`t express my idea well. I use your tutorial to calculation the free energy of a big system of my own,which is a big system of 24, atoms, so this speed is too slow for me and I am trying to run it on big clusters. Thanks any way. The simple decoupling procedure in the tutorial is likely not suitable for very large systems; by changing many degrees of freedom simultaneously in this way, convergence is exceptionally hard to achieve. I suspect the very large size of the DD cells is related to the couple-intramol parameter, which for large systems results in explicit pair interactions, which occur within the same DD cell. Refer to the manual for a more suitable setting and the reasons why you might want to adjust certain parameters. Good luck. -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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
