Re: [gmx-users] g_msd problem
On 5/18/13 4:32 PM, rajat desikan wrote: I have experienced something similar with large trajectories. This command got killed by 42 ns, with the same error. It is a 60 ns trajectory of a large membrane-protein system (approx 45 particles, Gromos 54A7 ff) with data stored every ps. g_msd -f analysis_60ns_pbcnojump.xtc -s analysis.tpr -o msd_popc_overall.xvg -lateral z -n index.ndx Both issues sound like memory problems. See http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume for advice. If reducing the number of frames allows the program to run successfully, you have your answer. In the OP's case, I would advise upgrading from version 4.0.3, which is ancient. At the very least, try 4.0.7, which is the terminal version in the 4.0.x series. Development is fluid and small bugs get fixed all the time, so using a version that is more than 4 years old may be asking for trouble. -Justin On Sun, May 19, 2013 at 1:57 AM, Yutian Yang wrote: Dear all, I am using g_msd to calculate diffusion coefficient of the centre of mass of single polymer chain with the following command: g_msd_mpi -f 1.trr -s eqm.tpr -n run.ndx -rmcomm -beginfit 5 -endfit 40 However, it often get killed for number of beads larger than 37, as shown below: Reading file eqm.tpr, VERSION 4.0.3 (single precision) Reading file eqm.tpr, VERSION 4.0.3 (single precision) Select a group to calculate mean squared displacement for: Group 0 ( System) has 13042 elements Group 1 (PEO) has37 elements Group 2 ( WF) has 1301 elements Group 3 ( W) has 11704 elements Group 4 ( WF_W) has 13005 elements Select a group: 1 Selected 1: 'PEO' Now select a group for center of mass removal: Group 0 ( System) has 13042 elements Group 1 (PEO) has37 elements Group 2 ( WF) has 1301 elements Group 3 ( W) has 11704 elements Group 4 ( WF_W) has 13005 elements Select a group: 1 Selected 1: 'PEO' trn version: GMX_trn_file (single precision) Reading frame 24000 time 24.000 Killed. Is it also a bug in the program or have I done something wrong on the command? Thank you! Best Regards Yutian Yang -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] g_msd problem
I have experienced something similar with large trajectories. This command got killed by 42 ns, with the same error. It is a 60 ns trajectory of a large membrane-protein system (approx 45 particles, Gromos 54A7 ff) with data stored every ps. g_msd -f analysis_60ns_pbcnojump.xtc -s analysis.tpr -o msd_popc_overall.xvg -lateral z -n index.ndx On Sun, May 19, 2013 at 1:57 AM, Yutian Yang wrote: > Dear all, > > I am using g_msd to calculate diffusion coefficient of the centre of mass > of single polymer chain with the following command: > g_msd_mpi -f 1.trr -s eqm.tpr -n run.ndx -rmcomm -beginfit 5 -endfit > 40 > > However, it often get killed for number of beads larger than 37, as shown > below: > > Reading file eqm.tpr, VERSION 4.0.3 (single precision) > Reading file eqm.tpr, VERSION 4.0.3 (single precision) > > Select a group to calculate mean squared displacement for: > Group 0 ( System) has 13042 elements > Group 1 (PEO) has37 elements > Group 2 ( WF) has 1301 elements > Group 3 ( W) has 11704 elements > Group 4 ( WF_W) has 13005 elements > Select a group: 1 > Selected 1: 'PEO' > > Now select a group for center of mass removal: > Group 0 ( System) has 13042 elements > Group 1 (PEO) has37 elements > Group 2 ( WF) has 1301 elements > Group 3 ( W) has 11704 elements > Group 4 ( WF_W) has 13005 elements > Select a group: 1 > Selected 1: 'PEO' > trn version: GMX_trn_file (single precision) > Reading frame 24000 time 24.000 Killed. > > Is it also a bug in the program or have I done something wrong on the > command? > > Thank you! > > Best Regards > Yutian Yang > > > > -- > 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 > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] g_msd problem
Dear all, I am using g_msd to calculate diffusion coefficient of the centre of mass of single polymer chain with the following command: g_msd_mpi -f 1.trr -s eqm.tpr -n run.ndx -rmcomm -beginfit 5 -endfit 40 However, it often get killed for number of beads larger than 37, as shown below: Reading file eqm.tpr, VERSION 4.0.3 (single precision) Reading file eqm.tpr, VERSION 4.0.3 (single precision) Select a group to calculate mean squared displacement for: Group 0 ( System) has 13042 elements Group 1 (PEO) has37 elements Group 2 ( WF) has 1301 elements Group 3 ( W) has 11704 elements Group 4 ( WF_W) has 13005 elements Select a group: 1 Selected 1: 'PEO' Now select a group for center of mass removal: Group 0 ( System) has 13042 elements Group 1 (PEO) has37 elements Group 2 ( WF) has 1301 elements Group 3 ( W) has 11704 elements Group 4 ( WF_W) has 13005 elements Select a group: 1 Selected 1: 'PEO' trn version: GMX_trn_file (single precision) Reading frame 24000 time 24.000 Killed. Is it also a bug in the program or have I done something wrong on the command? Thank you! Best Regards Yutian Yang -- 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: gmx-users Digest, Vol 109, Issue 112
Dear all, I am using g_msd to calculate diffusion coefficient of the centre of mass of single polymer chain with the following command: g_msd_mpi -f 1.trr -s eqm.tpr -n run.ndx -rmcomm -beginfit 5 -endfit 40 However, it often get killed for number of beads larger than 37, as shown below: Reading file eqm.tpr, VERSION 4.0.3 (single precision) Reading file eqm.tpr, VERSION 4.0.3 (single precision) Select a group to calculate mean squared displacement for: Group 0 ( System) has 13042 elements Group 1 (PEO) has37 elements Group 2 ( WF) has 1301 elements Group 3 ( W) has 11704 elements Group 4 ( WF_W) has 13005 elements Select a group: 1 Selected 1: 'PEO' Now select a group for center of mass removal: Group 0 ( System) has 13042 elements Group 1 (PEO) has37 elements Group 2 ( WF) has 1301 elements Group 3 ( W) has 11704 elements Group 4 ( WF_W) has 13005 elements Select a group: 1 Selected 1: 'PEO' trn version: GMX_trn_file (single precision) Reading frame 24000 time 24.000 Killed. Is it also a bug in the program or have I done something wrong on the command? Thank you! Best Regards Yutian Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of gmx-users-requ...@gromacs.org [gmx-users-requ...@gromacs.org] Sent: Saturday, May 18, 2013 2:48 PM To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 109, Issue 112 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. metadynamics (Sathish Kumar) 2. charmm in gromacs cut-offs (tarak karmakar) 3. R: [gmx-users] metadynamics (Spitaleri Andrea) 4. proceed from output of MD (Ewaru) 5. Add CS ions to system (Shima Arasteh) 6. Re: Re: REMD analysis (bharat gupta) 7. Re: proceed from output of MD (Ewaru) 8. Re: charmm in gromacs cut-offs (Justin Lemkul) -- Message: 1 Date: Sat, 18 May 2013 15:56:15 +0530 From: Sathish Kumar Subject: [gmx-users] metadynamics To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Sir, i want to learn about metadynamics, how to run metadynamics in gromacs.please suggest me in this regard. Thank you. -- regards M.SathishKumar -- Message: 2 Date: Sat, 18 May 2013 17:28:13 +0530 From: tarak karmakar Subject: [gmx-users] charmm in gromacs cut-offs To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Dear All, It seems the problem in the cut-off schemes while using charmm force field in gromacs persists even in the latest gromacs-4.6.1 version. Recently I have posted regarding this problem came in gromacs-4.5.5 version. If anybody has already tested this issue in the latest version, please leave a comment in the mailing list. The cut-off parameters I have used are as follows rlist = 1.2 rlistlong = 1.4 ; 7.3.10 Electrostatics coulombtype = PME rcoulomb= 1.2 ; 7.3.11 VdW vdwtype= switch rvdw = 1.2 rvdw-switch = 1.0 NOTE 3 [file md_sim_ann.mdp]: The switch/shift interaction settings are just for compatibility; you will get better performance from applying potential modifiers to your interactions! NOTE 4 [file md_sim_ann.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. NOTE 5 [file md_sim_ann.mdp]: The sum of the two largest charge group radii (0.079732) is larger than rlist (1.20) - rvdw (1.20) This part is reported as bug in gromacs -4.5.5 and required to be verified by users through their feedback http://redmine.gromacs.org/issues/1164 In this link it is showing affected version grom-4.6.1 !! Thanks and regards, Tarak -- Message: 3 Date: Sat, 18 May 2013 15:50:01 +0200 From: Spitaleri Andrea Subject: R: [gmx-users] metadynamics To: Discussion list for GROMACS users Message-ID: <685d68d01e4fc74ab398a2f494f4aa1f27dabda...@srexchmb01.sanraf.dom> Content-Type: text/plain; charset="us-ascii" Hi, have look to: http://www.plumed-code.org/ and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Geno
Re: [gmx-users] Re: REMD analysis
On Sat, May 18, 2013 at 5:17 PM, bharat gupta wrote: > Dear Sir, > > My main objective of carrying out REMD is to study peptide folding and if > possible to get some insight in protein design and folding. I read some > articles related to my work and they always show temp (replica_index) > graphs for 2-3 replicas , saying that the sufficient sampling had been > achieved. In my case I checked the replica_temp for first three replicas ( > https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png) ( > https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png) > https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png) > You've shown the same graph three times. > Almost all the three graphs are similar and the last 15ns shows that there > is no enough exchange (if I have analyzed correctly) ?? In this case the > acceptance ratio was fine and PE overlap was also good, but problem lies > with efficient sampling ?? Like I've been saying, acceptance does not assure enhanced sampling. > What shall I do in such a case ?? > Do some of the reading I've been suggesting? One of the papers shows that it is hard to get good sampling with just Met-enkephalin unless you design the temperature range for it. Mark On Sat, May 18, 2013 at 12:27 AM, Mark Abraham >wrote: > > > On Fri, May 17, 2013 at 4:26 PM, bharat gupta > >wrote: > > > > > Dear Sir, > > > > > > The the default bin width is 0.1 which I used for plotting the graphs. > > > > > > > That's nice. You need to decide what you need to do about it if you want > > graphs that look like those you see reported :-) > > > > > > > Another question is about your last reply to my thread "exchange > > acceptance > > > is a poor proxy for sampling efficiency". Sorry to ask this, but how to > > > check whether the sampling efficiency is optimal or not (what should be > > > optimal sampling efficiency) ?? > > > > > > > Ah, now here's the real question :-) Spacing the replicas for optimal > > *flow* is a difficult problem, even for toy peptides, see e.g. papers by > > Nadler and Hansmann. Merely accepting exchanges does not imply flow. The > > belief is that getting flow enhances sampling, but the latter is hard to > > demonstrate without showing that "simulation time to converged sampling" > > actually reduces. I'm not aware of anybody who's actually done that - but > > it would certainly be an advantage if your application is interested in > > data at a range of temperatures. > > > > Mark > > > > On Fri, May 17, 2013 at 11:10 PM, Mark Abraham > > >wrote: > > > > > > > Histograms 101: The smaller your bin width, the more variations you > > see. > > > > The more samples you have, the fewer variations you see. A histogram > > that > > > > does not mention either of this is a work of fiction. > > > > > > > > The number of degrees of freedom in the potential energy distribution > > is > > > > also a factor in whether the distribution will look smooth for a > given > > > bin > > > > width and number of samples. > > > > > > > > Mark > > > > > > > > On Fri, May 17, 2013 at 3:51 PM, bharat gupta < > > bharat.85.m...@gmail.com > > > > >wrote: > > > > > > > > > Dear Sir, > > > > > > > > > > I tried plotting the PE overlap using the following way :- > > > > > > > > > > 1. extract PE of each replica using g_energy > > > > > 2. get the PE distribution using g_analyze -f potential_0.xvg -dist > > > > > pot0.xvg > > > > > 3. used xmgrace to plot all the PE distribution graphs together. > > > > > > > > > > The same thing I did for temperature distribution for each replica. > > > > > > > > > > Here's the file for both PE overlap ( > > > > > https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png) > > > > > temp distribution ( > > > > https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png > > > > > ) > > > > > Is this the correct way ?? > > > > > > > > > > > > > > > But the plot doesnot look like this ( > > > > > > https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg > > ). > > > > Do i > > > > > have to normalize the data and then plot in order to get a smooth > > plot > > > > like > > > > > this one?? > > > > > > > > > > > > > > > Bharat > > > > > -- > > > > > 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 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 g
Aw: Re: [gmx-users] Expanding a .top file to have all connection information
Or just do it by hand and replace the lines in the .top with each protein chains .itp file. Stephan Gesendet: Freitag, 17. Mai 2013 um 16:17 Uhr Von: "Mark Abraham" An: "Discussion list for GROMACS users" Betreff: Re: [gmx-users] Expanding a .top file to have all connection information How does grompp -pp look? Mark On Fri, May 17, 2013 at 3:40 PM, davidjrosenman wrote: > Hello everyone, > > This may be a bit out of the purview of this list, but it can't hurt to > ask. > > Let me start from the beginning: I'm trying to take a structure/topology > that I generated with GROMACS tools and convert it to run with NAMD. The > problem is that this is a huge simulation box with many different atom > types > (homodimeric protein, water, lipids, ions), and I am having a lot of > trouble > generating a .psf file from the information I have. > > The current strategy I'm pursuing to accomplish this task is to use the > top2psf script: > http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/ > > The issue is that this script will only read what is explicitly written in > the top file. All of the include records will be ignored, as will multiple > molecules. So, the output is a psf suitable ONLY for the first chain of my > dimer. I want a psf that will include all components of my structure, > including the lipids, waters, etc. > > So, I ask, is there a way to expand a topology to explicitly get all of the > connectivities in a structure? I figure this information must be contained > in the .tpr file, but that's neither human readable nor compatible with > top2psf. > > If you have any advice for that, or for the larger problem at hand, I would > appreciate it. Thank you very much! > > Cheers, > David Rosenman > Grad Student, Rensselaer Polytechnic Institute > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Expanding-a-top-file-to-have-all-connection-information-tp5008345.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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 -- 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] Add CS ions to system
On 5/18/13 10:02 AM, Shima Arasteh wrote: Hi all, I want to add CS ions to my system by genion but it seems impossible when go through the EM. The molecule section in my top file is: Protein_chain_A 1 Protein_chain_B 1 POPC238 SOL 20406 NA 681 CL 702 CS 19 The commands to neutralize and adding CsCl are as follow: Adding ions: #grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr #genion -s ions.tpr -o system_solv_ions.gro -p topol.top -conc 1 -neutral Adding 19 pairs of CsCl: #grompp -f ions.mdp -c system_solv_ions.gro -p topol.top -o ions_CsCl.tpr #genion -s ions_CsCl.tpr -o system_solv_ions_CsCl.gro -p topol.top -pname CS -np 19 -nname CL -nn 19 EM: And fatal error as I get is: #grompp -f minim.mdp -c system_solv_ions_CsCl.gro -p topol.top -o minim.tpr Fatal error: No such moleculetype CS But I see the CS ion in residuetypes.dat which exist in my directory : CSIon So what's the reason? If it is related to the version of applied GROMACS? I am working with 4.5.5 GROMACS and CHARMM 36 FF. All that residuetypes.dat indicates is that Gromacs, in general, has the ability to understand that Cs are ions. That is not to say that every force field has parameters for Cs. That's your problem - the CHARMM force field you have doesn't include parameters for a moleculetype named "CS" (look at its ions.itp file), though CHARMM27 packaged with Gromacs does have these parameters. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] Re: Running Pull Code
On 5/18/13 1:23 AM, Shima Arasteh wrote: If I skip the pulling code step, how could I generate configurations while there are one ion in each window? Am I supposed to save my favorite snapshots during MD simulation trajectory? You can generate configurations in any way you see fit. SMD is just one possibility. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] charmm in gromacs cut-offs
On 5/18/13 7:58 AM, tarak karmakar wrote: Dear All, It seems the problem in the cut-off schemes while using charmm force field in gromacs persists even in the latest gromacs-4.6.1 version. Recently I have posted regarding this problem came in gromacs-4.5.5 version. If anybody has already tested this issue in the latest version, please leave a comment in the mailing list. The cut-off parameters I have used are as follows rlist = 1.2 rlistlong = 1.4 ; 7.3.10 Electrostatics coulombtype = PME rcoulomb= 1.2 ; 7.3.11 VdW vdwtype= switch rvdw = 1.2 rvdw-switch = 1.0 NOTE 3 [file md_sim_ann.mdp]: The switch/shift interaction settings are just for compatibility; you will get better performance from applying potential modifiers to your interactions! NOTE 4 [file md_sim_ann.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. NOTE 5 [file md_sim_ann.mdp]: The sum of the two largest charge group radii (0.079732) is larger than rlist (1.20) - rvdw (1.20) This part is reported as bug in gromacs -4.5.5 and required to be verified by users through their feedback http://redmine.gromacs.org/issues/1164 In this link it is showing affected version grom-4.6.1 !! There are a lot of conditionals that are evaluated and probably (as Mark has indicated) some of them are conflicting. What you have posted above seems correct from my interpretation of everything I have read about using CHARMM. Since all you are getting are notes (rather than errors), you shouldn't have any problems. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
[gmx-users] Re: proceed from output of MD
Hey, I have figured that out! My bad! :D Thank you. Best regards -- View this message in context: http://gromacs.5086.x6.nabble.com/proceed-from-output-of-MD-tp5008364p5008368.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: REMD analysis
Dear Sir, My main objective of carrying out REMD is to study peptide folding and if possible to get some insight in protein design and folding. I read some articles related to my work and they always show temp (replica_index) graphs for 2-3 replicas , saying that the sufficient sampling had been achieved. In my case I checked the replica_temp for first three replicas ( https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png) ( https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png) https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png) Almost all the three graphs are similar and the last 15ns shows that there is no enough exchange (if I have analyzed correctly) ?? In this case the acceptance ratio was fine and PE overlap was also good, but problem lies with efficient sampling ?? What shall I do in such a case ?? On Sat, May 18, 2013 at 12:27 AM, Mark Abraham wrote: > On Fri, May 17, 2013 at 4:26 PM, bharat gupta >wrote: > > > Dear Sir, > > > > The the default bin width is 0.1 which I used for plotting the graphs. > > > > That's nice. You need to decide what you need to do about it if you want > graphs that look like those you see reported :-) > > > > Another question is about your last reply to my thread "exchange > acceptance > > is a poor proxy for sampling efficiency". Sorry to ask this, but how to > > check whether the sampling efficiency is optimal or not (what should be > > optimal sampling efficiency) ?? > > > > Ah, now here's the real question :-) Spacing the replicas for optimal > *flow* is a difficult problem, even for toy peptides, see e.g. papers by > Nadler and Hansmann. Merely accepting exchanges does not imply flow. The > belief is that getting flow enhances sampling, but the latter is hard to > demonstrate without showing that "simulation time to converged sampling" > actually reduces. I'm not aware of anybody who's actually done that - but > it would certainly be an advantage if your application is interested in > data at a range of temperatures. > > Mark > > On Fri, May 17, 2013 at 11:10 PM, Mark Abraham > >wrote: > > > > > Histograms 101: The smaller your bin width, the more variations you > see. > > > The more samples you have, the fewer variations you see. A histogram > that > > > does not mention either of this is a work of fiction. > > > > > > The number of degrees of freedom in the potential energy distribution > is > > > also a factor in whether the distribution will look smooth for a given > > bin > > > width and number of samples. > > > > > > Mark > > > > > > On Fri, May 17, 2013 at 3:51 PM, bharat gupta < > bharat.85.m...@gmail.com > > > >wrote: > > > > > > > Dear Sir, > > > > > > > > I tried plotting the PE overlap using the following way :- > > > > > > > > 1. extract PE of each replica using g_energy > > > > 2. get the PE distribution using g_analyze -f potential_0.xvg -dist > > > > pot0.xvg > > > > 3. used xmgrace to plot all the PE distribution graphs together. > > > > > > > > The same thing I did for temperature distribution for each replica. > > > > > > > > Here's the file for both PE overlap ( > > > > https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png) > > > > temp distribution ( > > > https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png > > > > ) > > > > Is this the correct way ?? > > > > > > > > > > > > But the plot doesnot look like this ( > > > > https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg > ). > > > Do i > > > > have to normalize the data and then plot in order to get a smooth > plot > > > like > > > > this one?? > > > > > > > > > > > > Bharat > > > > -- > > > > 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 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 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 mailing listgmx-users@gromacs.org > http
[gmx-users] Add CS ions to system
Hi all, I want to add CS ions to my system by genion but it seems impossible when go through the EM. The molecule section in my top file is: Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 20406 NA 681 CL 702 CS 19 The commands to neutralize and adding CsCl are as follow: Adding ions: #grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr #genion -s ions.tpr -o system_solv_ions.gro -p topol.top -conc 1 -neutral Adding 19 pairs of CsCl: #grompp -f ions.mdp -c system_solv_ions.gro -p topol.top -o ions_CsCl.tpr #genion -s ions_CsCl.tpr -o system_solv_ions_CsCl.gro -p topol.top -pname CS -np 19 -nname CL -nn 19 EM: And fatal error as I get is: #grompp -f minim.mdp -c system_solv_ions_CsCl.gro -p topol.top -o minim.tpr Fatal error: No such moleculetype CS But I see the CS ion in residuetypes.dat which exist in my directory : CS Ion So what's the reason? If it is related to the version of applied GROMACS? I am working with 4.5.5 GROMACS and CHARMM 36 FF. Thanks. Would you give me any suggestions? Sincerely, Shima -- 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] proceed from output of MD
Hi, I have run a 20ns MD simulation on my protein structure and about to proceed with Autodock. I am wondering if I have missed anything. The output of the file is gro, so I converted it to a pdb file. Then, when I process it with Autodock Tools, all I get is the water molecules surrounding my protein in a box. How can I get rid of the box? Please advice. Thanking you in advance. Best regards -- View this message in context: http://gromacs.5086.x6.nabble.com/proceed-from-output-of-MD-tp5008364.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
R: [gmx-users] metadynamics
Hi, have look to: http://www.plumed-code.org/ and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics Basilica San Raffaele, 3P 34R Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ www.biomolnmr.org Tel: 0039-0226434348 Fax: 0039-0226434153 -- LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO. AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 07636600962 info:www.5xmi...@hsr.it - www.5xmille.org Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di Sathish Kumar [sathishk...@gmail.com] Inviato: sabato 18 maggio 2013 12.26 A: Discussion list for GROMACS users Oggetto: [gmx-users] metadynamics Sir, i want to learn about metadynamics, how to run metadynamics in gromacs.please suggest me in this regard. Thank you. -- regards M.SathishKumar -- 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 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] charmm in gromacs cut-offs
Dear All, It seems the problem in the cut-off schemes while using charmm force field in gromacs persists even in the latest gromacs-4.6.1 version. Recently I have posted regarding this problem came in gromacs-4.5.5 version. If anybody has already tested this issue in the latest version, please leave a comment in the mailing list. The cut-off parameters I have used are as follows rlist = 1.2 rlistlong = 1.4 ; 7.3.10 Electrostatics coulombtype = PME rcoulomb= 1.2 ; 7.3.11 VdW vdwtype= switch rvdw = 1.2 rvdw-switch = 1.0 NOTE 3 [file md_sim_ann.mdp]: The switch/shift interaction settings are just for compatibility; you will get better performance from applying potential modifiers to your interactions! NOTE 4 [file md_sim_ann.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. NOTE 5 [file md_sim_ann.mdp]: The sum of the two largest charge group radii (0.079732) is larger than rlist (1.20) - rvdw (1.20) This part is reported as bug in gromacs -4.5.5 and required to be verified by users through their feedback http://redmine.gromacs.org/issues/1164 In this link it is showing affected version grom-4.6.1 !! Thanks and regards, Tarak -- 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] metadynamics
Sir, i want to learn about metadynamics, how to run metadynamics in gromacs.please suggest me in this regard. Thank you. -- regards M.SathishKumar -- 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] how to add angle_restraints and dihedral_restraints for atoms belonging to two different molecules
On Sat, May 18, 2013 at 10:20 AM, jnsong wrote: > Dear all, > > Recently, I want to add angle_restraints and dihedral_restraints for atoms > in two separate molecules, that is, inter-molecular restraints, not > intra-molecular restraints. > > I add the following into my .top file: > [ angle_restraints ] > ; i jkltype theta0 fc multiplicity > 20 22 47 501 0.0 1500 1 > > [ dihedral_restraints ] > ; ij kltype label phi dphi kfac power >25 2851 52 1 1 180 0 1 2 > > But it give errors: > "Fatal error: > [ file ang_res.itp, line 5 ]: > Atom index (47) in angle_restraints out of bounds (1-24). > This probably means that you have inserted topology section > "angle_restraints" > in a part belonging to a different molecule than you intended to." > > Atom 20/22 belongs to one molecule, and Atom 47/50 belongs to another > molecule. The same situation is for atom 25/28 and atom 51/52. > > I guess this error comes from the fact that I have two separate molecules > in my simulation system, thus topol_Protein.itp and topol_Protein2.itp are > produced when using pdb2gmx. Atom 47 in .gro file has atom number 17 in > topol_Protein2.itp. Thus it gives the error that Atom index (47) in > angle_restraints out of bounds! > > Additionally, [ angle_restraints] and [dihedral_restraints] seems for the > intra-molecular interaction definitions. > > Would you please tell me how to add angle and dihedral restraints for the > atoms that belong to two different molecules? > You need both molecules in the same [moleculetype], since the restraint directives require this. pdb2gmx -h will help here. 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
Re: [gmx-users] ionic liquids - viscosity via green kubo relation
Krzysztof, You were indeed correct to suggest augmenting the ACF window. For ionic liquids, I have seen ACF windows that are around 500 ps, thank you for your suggestion !!! 2013/5/7 Krzysztof Murzyn > Hello, > > I would try to extend ACF window (10, 50, 200ps) but not too much since you > might end with integrating noise which would lead to overestimation of > viscosity. For water, 4ps seems to be ok but your liquid might have longer > ACF tail so you are actually getting seriously underestimated viscosity. > You should also run calculations for Pxz, Pyz, (Pxx-Pyy)/2 and (Pyy-Pzz)/2 > to improve statistics. > > Regards, > km. > > > On Tue, May 7, 2013 at 4:13 PM, Thomas P wrote: > > > Hello all, > > > > I have a periodic system of composed of 200 pairs of > > 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide. I equilibrate > > the system for 1.5 ns to the appropriate density under 1 atm and 300 K in > > the NPT ensemble. As a sidenote, I do obtain the density cited in the > > literature for the system and force field in question. > > > > Once equilibrated, I pass into the NVE ensemble, and store the the Pxy > > pressure tensor component of the entire group of atoms. I am doing this > to > > calculate the viscosity of my liquid using the Green-Kubo relation. > > > > I have been calculating the Stress Autocorrelation Function (SACF) for > Pxy > > using Matlab. The autocorrelation window is 4 ps, and data was stored > over > > a 1 ns production run every 5 fs (200 000 data points). I know a 1 ns > run > > may be slightly short for an ionic liquid, but the simulations take > quite a > > long time already, and I therefore wanted to rule out any other issues > > before doing a longer run. > > > > The SACF (normalized to 1) that I obtain is attached, and I do not really > > know what to make of it; it is not smooth at all (quite jaggedy in > fact!). > > Furthermore, when I integrate to compute the viscosity (I do not > integrate > > the normalized curve obviously), I obtain around 6 cP which is 2 orders > of > > magnitude too small... > > > > I am quite sure there are no errors in the parameters of my force field, > > maybe someone can suggest something that I may have missed? > > > > -- > > 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 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 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] how to add angle_restraints and dihedral_restraints for atoms belonging to two different molecules
Dear all, Recently, I want to add angle_restraints and dihedral_restraints for atoms in two separate molecules, that is, inter-molecular restraints, not intra-molecular restraints. I add the following into my .top file: [ angle_restraints ] ; i jkltype theta0 fc multiplicity 20 22 47 501 0.0 1500 1 [ dihedral_restraints ] ; ij kltype label phi dphi kfac power 25 2851 52 1 1 180 0 1 2 But it give errors: "Fatal error: [ file ang_res.itp, line 5 ]: Atom index (47) in angle_restraints out of bounds (1-24). This probably means that you have inserted topology section "angle_restraints" in a part belonging to a different molecule than you intended to." Atom 20/22 belongs to one molecule, and Atom 47/50 belongs to another molecule. The same situation is for atom 25/28 and atom 51/52. I guess this error comes from the fact that I have two separate molecules in my simulation system, thus topol_Protein.itp and topol_Protein2.itp are produced when using pdb2gmx. Atom 47 in .gro file has atom number 17 in topol_Protein2.itp. Thus it gives the error that Atom index (47) in angle_restraints out of bounds! Additionally, [ angle_restraints] and [dihedral_restraints] seems for the intra-molecular interaction definitions. Would you please tell me how to add angle and dihedral restraints for the atoms that belong to two different molecules? Thank you very much! Best wishes! Jianing Song -- 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
