Re: [gmx-users] Re: Running Pull Code
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? Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Friday, May 17, 2013 4:02 PM Subject: Re: [gmx-users] Re: Running Pull Code On 5/17/13 7:16 AM, Shima Arasteh wrote: > Thanks for your reply. > It' s around 5 nano seconds that I ran equilibration time on the system, and > the average pressure I see as a result, seems sensible. However I am not sure > if this criteria is sufficient? Others suggest to evaluate the box-dimension > changes using g_energy code to judge of sufficient equilibration time. > The box vectors won't tell you anything more than the pressure will since they're related quantities. The better question is, "What is a suitable starting structure for the system of interest?" The umbrella sampling tutorial (which everyone seems to take at literal face value as the only way to do things, which it is decidedly not) presents a simple, easy-to-understand method. In the paper I did (upon which I based the tutorial), I simulated the protofibril structures for 100 ns before I was confident they were suitably stable and representative of viable structures for doing SMD and US. Your mileage will vary and depends on the quality of the starting structure and what it is that you hope to determine. There is no magic recipe that is universal. -Justin > I appreciate your suggestion. > > > Sincerely, > Shima > > > - Original Message - > From: Thomas Schlesier > To: gmx-users@gromacs.org > Cc: > Sent: Friday, May 17, 2013 3:30 PM > Subject: [gmx-users] Re: Running Pull Code > > The three steps (EM, NVT and NPT) are to equilibrate the system. How > much time these steps need depends on the system. But i would assume a > ouple of nanosecounds are sufficient for most systems. You could look > into the literature, how long other people equilibrate systems which are > similar to ours. > If the system is equilibrated, you an start to perform the pulling > simulation to obtain the individual structure for the later umbrella > sampling. > > Greetings > Thomas > > Am 17.05.2013 07:46, schrieb gmx-users-requ...@gromacs.org: >> Hi, >> >> I have a system composed of POPC/peptide/water/ions. I aim to study ion >> conduction through the peptide using umbrella sampling. >> I built the system and ran EM, NVT, NPT successfully, but have not run md >> yet. I' d like to know if the system is required of passing a few >> nanoseconds md? Or I might be able to go to Umbrella Sampling straight after >> NPT? >> As I studied in Justin's tutorial, running pull code is done after some >> typical steps of every simulation ( EM, NVT, NPT). But I dont know if is >> correct generally for other systems as well? >> >> Would you please give me any suggestions? >> >> >> Thanks in advance. >> Sincerely, >> Shima? > -- 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] Inconsistent results in different clusters and cores
@ Justin and Mark, Do you have any idea about the rlist used by Bjelkmar et. al. 'Implementation of charmm in gromacs'? I see, they have performed their simulations in gromacs-4.1 version. I'm not sure about whether in that version the problem persisted or not. I'm sorry if this mail went to you twice. Facing lot of problems, here, in mail delivery failure. Thanks, Tarak On Fri, May 17, 2013 at 6:22 PM, tarak karmakar wrote: > @ Justin and Mark, > > Do you have any idea about the rlist used by Bjelkmar et. al. > 'Implementation of charmm in gromacs'? I see, they have performed > their simulations in gromacs-4.1 version. I'm not sure about whether > in that version the problem persisted or not. > > Tarak > > On Fri, May 17, 2013 at 5:42 PM, tarak karmakar wrote: >> I am extremely sorry for spaming the mail box. It was quite >> unintentionally. Believe me I was getting the following error every >> time while sending the mail. >> >> Final-Recipient: rfc822; jaanus.k...@eesti.ee >> Action: failed >> Status: 5.0.0 >> Diagnostic-Code: X-Postfix; mail forwarding loop for jaanus.k...@eesti.ee >> >> Tarak >> >> >> -- Forwarded message -- >> From: tarak karmakar >> To: Discussion list for GROMACS users >> Cc: >> Date: Fri, 17 May 2013 15:50:25 +0530 >> Subject: Re: [gmx-users] Inconsistent results in different clusters and cores >> >> On Fri, May 17, 2013 at 5:36 PM, Mark Abraham >> wrote: >>> On Fri, May 17, 2013 at 1:23 PM, Justin Lemkul wrote: >>> On 5/17/13 6:20 AM, tarak karmakar wrote: > I have read the 'implementation of charmm in gromacs' by bjelkmar, > JCTC. There they have used following cut-offs > coulombtype=PME > rcoulomb=1.2 > vdwtype=switch > rvdw=1.2 > rvdw-switch=1.0 > > I am not sure about rlist. > > It's really unnecessary to spam the list with a dozen requests that ask the same question. By definition, with PME, rlist = rcoulomb. For CHARMM, use rlistlong = 1.4; the message that is printed below is an error that has been fixed in newer versions. >>> >>> >>> Are you sure? Looking at the logic in src/mdlib/read_ir.c, I could not see >>> how Tarak's input could have led (correctly) to that note from grompp. I am >>> thinking that >>> https://github.com/gromacs/gromacs/blob/release-4-5-patches/src/kernel/readir.c#L170 >>> is >>> setting rlistlong = rlist, and so >>> https://github.com/gromacs/gromacs/blob/release-4-5-patches/src/kernel/readir.c#L586 >>> gets >>> double-crossed. >>> >>> (Note that http://redmine.gromacs.org/issues/1164 pertained to a slightly >>> different issue.) >>> >>> 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 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] Tryptophan rings are not connected in visualization
On 5/17/13 10:08 PM, Shima Arasteh wrote: Hi, I am simulating a system composed if POPC , peptide, waters and ions. I used the InflateGRO methodology to construct the system. There are 2 Tryptophan residues in my peptide. Each Tryptophan has 2rings connected from one side. After inflategro one of the Tryptophan rings is normal, but the other is not because What I see them in vmd, there are 2rings remain close to eachother but the expected bonds between them are not visible. The top file shows the correct bonds and angles and ... . I ran EM, NVT, NPT, and thought this problem would be solved but it is still as well as before. The EM was also ok and did not show high enegy or crash. Does this problem relate to the vmd and its algorithms? Or there is a problem with my system. http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds The topology is definitive. VMD is not. How would the rings look usual? How could I solve it? Run EM. InflateGRO should not have messed with the coordinates though. If the bad geometry is a result of EM, that means you have really nasty forces somewhere in the system. -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 5/17/13 8:25 AM, Shima Arasteh wrote: Thanks for your reply. In fact, I plan to study ion conduction through the peptide inserted in lipid membrane and acting as an ion channel. According to the literature, an ion across the membrane in less than 20 ns. Can I decide upon this information to apply pull code? You simulated the protofibril structures for 100 ns, in another article 25 ns. Ok, if there is not any universal recipe for it, what do you suggest me? Try and error? Assess the literature thoroughly. Basing your plan on only one paper may not be the most productive way to go. See what many do, and base what you try off of what you find. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Friday, May 17, 2013 4:02 PM Subject: Re: [gmx-users] Re: Running Pull Code On 5/17/13 7:16 AM, Shima Arasteh wrote: Thanks for your reply. It' s around 5 nano seconds that I ran equilibration time on the system, and the average pressure I see as a result, seems sensible. However I am not sure if this criteria is sufficient? Others suggest to evaluate the box-dimension changes using g_energy code to judge of sufficient equilibration time. The box vectors won't tell you anything more than the pressure will since they're related quantities. The better question is, "What is a suitable starting structure for the system of interest?" The umbrella sampling tutorial (which everyone seems to take at literal face value as the only way to do things, which it is decidedly not) presents a simple, easy-to-understand method. In the paper I did (upon which I based the tutorial), I simulated the protofibril structures for 100 ns before I was confident they were suitably stable and representative of viable structures for doing SMD and US. Your mileage will vary and depends on the quality of the starting structure and what it is that you hope to determine. There is no magic recipe that is universal. -Justin I appreciate your suggestion. Sincerely, Shima - Original Message - From: Thomas Schlesier To: gmx-users@gromacs.org Cc: Sent: Friday, May 17, 2013 3:30 PM Subject: [gmx-users] Re: Running Pull Code The three steps (EM, NVT and NPT) are to equilibrate the system. How much time these steps need depends on the system. But i would assume a ouple of nanosecounds are sufficient for most systems. You could look into the literature, how long other people equilibrate systems which are similar to ours. If the system is equilibrated, you an start to perform the pulling simulation to obtain the individual structure for the later umbrella sampling. Greetings Thomas Am 17.05.2013 07:46, schrieb gmx-users-requ...@gromacs.org: Hi, I have a system composed of POPC/peptide/water/ions. I aim to study ion conduction through the peptide using umbrella sampling. I built the system and ran EM, NVT, NPT successfully, but have not run md yet. I' d like to know if the system is required of passing a few nanoseconds md? Or I might be able to go to Umbrella Sampling straight after NPT? As I studied in Justin's tutorial, running pull code is done after some typical steps of every simulation ( EM, NVT, NPT). But I dont know if is correct generally for other systems as well? Would you please give me any suggestions? Thanks in advance. Sincerely, Shima? -- 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] Tryptophan rings are not connected in visualization
Hi, I am simulating a system composed if POPC , peptide, waters and ions. I used the InflateGRO methodology to construct the system. There are 2 Tryptophan residues in my peptide. Each Tryptophan has 2rings connected from one side. After inflategro one of the Tryptophan rings is normal, but the other is not because What I see them in vmd, there are 2rings remain close to eachother but the expected bonds between them are not visible. The top file shows the correct bonds and angles and ... . I ran EM, NVT, NPT, and thought this problem would be solved but it is still as well as before. The EM was also ok and did not show high enegy or crash. Does this problem relate to the vmd and its algorithms? Or there is a problem with my system. How would the rings look usual? How could I solve it? Thanks in advance. 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
Re: [gmx-users] compile Gromacs using Cray compilers
Cray's compiler is largely/wholly untested. I'd suggest you use the version of gcc that you know works. For use on a big cluster, you probably don't want Thread MPI anyway. Does cmake -DGMX_MPI work? Mark On Sat, May 18, 2013 at 12:01 AM, Humayun Arafat wrote: > Hi, > > > I need some help for the compilation of gromacs using Cray compilers(CCE). > > I can compile gromacs using GNU compilers but not using CCE. > > I am using gromacs 4.6 and cmake 2.8.4 on Cray XE6 > > > > After doing cmake, when I try to do make, I am getting this error. > > > > CC-20 craycc: ERROR File = > /home/users/me/gromacs/include/thread_mpi/atomic.h, Line = 202 > > The identifier "tMPI_Thread_mutex_t" is undefined. > > static tMPI_Thread_mutex_t tMPI_Atomic_mutex = > TMPI_THREAD_MUTEX_INITIALIZER; > > ^ > > > > Then I checked that the cmake configuration had errors for this atomic.h > header file. > > It does not find any atomic operations for cray compilers. > > Inside this header file, I see that there is nothing for Cray compilers. > > It has GNU,Intel, xlc…. > > My guess is that probably it is not adding any atomic header file for CCE. > > > > > Please suggest me some ways to fix this. > > Thank you for your help. > > > Thanks > > Humayun > -- > 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] compile Gromacs using Cray compilers
Hi, I need some help for the compilation of gromacs using Cray compilers(CCE). I can compile gromacs using GNU compilers but not using CCE. I am using gromacs 4.6 and cmake 2.8.4 on Cray XE6 After doing cmake, when I try to do make, I am getting this error. CC-20 craycc: ERROR File = /home/users/me/gromacs/include/thread_mpi/atomic.h, Line = 202 The identifier "tMPI_Thread_mutex_t" is undefined. static tMPI_Thread_mutex_t tMPI_Atomic_mutex = TMPI_THREAD_MUTEX_INITIALIZER; ^ Then I checked that the cmake configuration had errors for this atomic.h header file. It does not find any atomic operations for cray compilers. Inside this header file, I see that there is nothing for Cray compilers. It has GNU,Intel, xlc…. My guess is that probably it is not adding any atomic header file for CCE. Please suggest me some ways to fix this. Thank you for your help. Thanks Humayun -- 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] visualizing the system
On Fri, May 17, 2013 at 10:21 PM, Shima Arasteh wrote: > > Hi, > I am simulating a system composed if POPC , peptide, waters and ions. > I used the InflateGRO methodology to construct the system. > There are 2 phenylalanine residues in my peptide. Each phenyl has 2rings > connected from one side. I don't understand. Phenylalanine has a single aromatic ring. > After inflategro one of the phenyl rings is normal, but the other is not > because What I see them in vmd, there are 2rings remain close to eachother > but the expected bonds between them are not visible. > Two phenylalanine residues are not expected to bond. > The top file shows the correct bonds and angles and ... . > I ran EM, NVT, NPT, and thought this problem would be solved but it is > still as well as before. > The EM was also ok and did not show high enegy or crash. > Does this problem relate to the vmd and its algorithms? Or there is a > problem with my system. > How would the rings look usual? How could I solve it? > Your description of your expectations of phenylalanine do not seem to make sense. :-) 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] visualizing the system
Hi, I am simulating a system composed if POPC , peptide, waters and ions. I used the InflateGRO methodology to construct the system. There are 2 phenylalanine residues in my peptide. Each phenyl has 2rings connected from one side. After inflategro one of the phenyl rings is normal, but the other is not because What I see them in vmd, there are 2rings remain close to eachother but the expected bonds between them are not visible. The top file shows the correct bonds and angles and ... . I ran EM, NVT, NPT, and thought this problem would be solved but it is still as well as before. The EM was also ok and did not show high enegy or crash. Does this problem relate to the vmd and its algorithms? Or there is a problem with my system. How would the rings look usual? How could I solve it? Thanks in advance. 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
Re: [gmx-users] Expanding a .top file to have all connection information
On Fri, May 17, 2013 at 4:28 PM, David Rosenman wrote: > This is a good idea, but it doesn't work. It produces a more detailed .top > file with force field parameters, but still, only the connectivities of the > protein are provided. What "connectivities" are missing? > top2psf has no idea what to do with this file, by the > way. > > Would it help for me to provide the pre-processed and post-processed top > files? > Sure, but attachments will generally be rejected. Use a file sharing service. Mark > > Cheers, > David > > > On Fri, May 17, 2013 at 10:17 AM, Mark Abraham >wrote: > > > How does grompp -pp look? > > > > Mark > > > > > > On Fri, May 17, 2013 at 3:40 PM, davidjrosenman < > davidjrosen...@gmail.com > > >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 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://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
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 > >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://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] Expanding a .top file to have all connection information
This is a good idea, but it doesn't work. It produces a more detailed .top file with force field parameters, but still, only the connectivities of the protein are provided. top2psf has no idea what to do with this file, by the way. Would it help for me to provide the pre-processed and post-processed top files? Cheers, David On Fri, May 17, 2013 at 10:17 AM, Mark Abraham wrote: > 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 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
Re: [gmx-users] Re: REMD analysis
Dear Sir, The the default bin width is 0.1 which I used for plotting the graphs. 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) ?? 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 >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
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 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
Re: [gmx-users] Re: REMD analysis
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 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
Re: [gmx-users] Re: REMD analysis
What do you not like in your distributions? What are your looking for in these distributions? I am not sure what you are expecting from the list here … your distributions are fine, but, as Mark noted, it does not mean your simulation and sampling will be optimal … On May 17, 2013, at 3:51 PM, bharat gupta 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
Re: [gmx-users] Comparing Gromacs versions
On Fri, May 17, 2013 at 2:48 PM, Djurre de Jong-Bruinink wrote: > > >>The answer is in the log files, in particular the performance summary >>should indicate where is the performance difference. If you post your >>log files somewhere we can probably give further tips on optimizing >>your run configurations. > > > I put the log files for 72 CPUs, using GMX455, GMX461+group and GMX461+verlet > here: > http://md.chem.rug.nl/~djurre/logs/N6_gmx455.log > http://md.chem.rug.nl/~djurre/logs/N6_gmx461_group.log > http://md.chem.rug.nl/~djurre/logs/N6_gmx461_verlet.log That tells much more. > It would be great if you could point out some possible optimizations. Here you go: - You seem to be using 2 fs time-steps so you don't need to constrain all bonds, constraining only h-bonds is enough. This will reduce the cell size requirement posed by LINCS and will allow further decomposition. Additionally, you can also tweak the LINCS order and iteration. - With the Verlet scheme you can use OpenMP parallelization to reduce the pressure on domain-decomposition, e.g. by using 2 OpenMP threads (at least for PP) you'd need only 24 domains instead of 48. OpenMP parallelization is not very efficient on the old-ish AMD processors you are using, but 2 threads/MPI ranks should still help at very high parallelization (<200 atoms/core). - On the AMD Istambul (K10) processors that you are using gcc generates rather poor non-bonded kernel code. icc will make the non-bondeds run 10-20% faster. - With Verlet scheme you can safely increase nstlist to higher values so already at 72 cores and especially at higher core count 12,15, or even 20 might give better performance. - Your 4.6 group scheme run shows large PP-PME imbalance, try increasing the number of PME ranks! > > >>Note that with such a small system the scaling with the group scheme >>surely becomes limited by imbalance and probably it won't scale much >>further than 72 cores. At the same time, simulations with the verlet >>scheme have shown scaling to below 100 atoms/core. > > I tried running on 84 cpus (56PP cores=400 atoms/PP core), but I did get an > domain decomposition error. Maybe I could optimize -rcon and -dds further, > however although the scaling to more CPUs is better with the verlet scheme, I > think you will never win: with 72 CPUs Verlet is almost as fast as with > group at 60 CPUs, however compared to 24 cpus the scaling per CPU is already > down to 60%. > > But as Mark Abraham mentioned, it might be that my system is just to small to > get the advantage of scaling that will be there in larger systems. As I mentioned before, you *should* be able to use 2x more cores (or perhaps even more), but of course the parallel efficiency will decrease. Cheers, -- Szilard > > > Groetnis, > Djurre > > -- > 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] Re: REMD analysis
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] Expanding a .top file to have all connection information
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 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] Inconsistent results in different clusters and cores
@ Justin and Mark, Do you have any idea about the rlist used by Bjelkmar et. al. 'Implementation of charmm in gromacs'? I see, they have performed their simulations in gromacs-4.1 version. I'm not sure about whether in that version the problem persisted or not. Tarak On Fri, May 17, 2013 at 5:42 PM, tarak karmakar wrote: > I am extremely sorry for spaming the mail box. It was quite > unintentionally. Believe me I was getting the following error every > time while sending the mail. > > Final-Recipient: rfc822; jaanus.k...@eesti.ee > Action: failed > Status: 5.0.0 > Diagnostic-Code: X-Postfix; mail forwarding loop for jaanus.k...@eesti.ee > > Tarak > > > -- Forwarded message -- > From: tarak karmakar > To: Discussion list for GROMACS users > Cc: > Date: Fri, 17 May 2013 15:50:25 +0530 > Subject: Re: [gmx-users] Inconsistent results in different clusters and cores > > On Fri, May 17, 2013 at 5:36 PM, Mark Abraham > wrote: >> On Fri, May 17, 2013 at 1:23 PM, Justin Lemkul wrote: >> >>> >>> >>> On 5/17/13 6:20 AM, tarak karmakar wrote: >>> I have read the 'implementation of charmm in gromacs' by bjelkmar, JCTC. There they have used following cut-offs coulombtype=PME rcoulomb=1.2 vdwtype=switch rvdw=1.2 rvdw-switch=1.0 I am not sure about rlist. >>> It's really unnecessary to spam the list with a dozen requests that ask >>> the same question. >>> >>> By definition, with PME, rlist = rcoulomb. For CHARMM, use rlistlong = >>> 1.4; the message that is printed below is an error that has been fixed in >>> newer versions. >> >> >> Are you sure? Looking at the logic in src/mdlib/read_ir.c, I could not see >> how Tarak's input could have led (correctly) to that note from grompp. I am >> thinking that >> https://github.com/gromacs/gromacs/blob/release-4-5-patches/src/kernel/readir.c#L170 >> is >> setting rlistlong = rlist, and so >> https://github.com/gromacs/gromacs/blob/release-4-5-patches/src/kernel/readir.c#L586 >> gets >> double-crossed. >> >> (Note that http://redmine.gromacs.org/issues/1164 pertained to a slightly >> different issue.) >> >> 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 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] Comparing Gromacs versions
>The answer is in the log files, in particular the performance summary >should indicate where is the performance difference. If you post your >log files somewhere we can probably give further tips on optimizing >your run configurations. I put the log files for 72 CPUs, using GMX455, GMX461+group and GMX461+verlet here: http://md.chem.rug.nl/~djurre/logs/N6_gmx455.log http://md.chem.rug.nl/~djurre/logs/N6_gmx461_group.log http://md.chem.rug.nl/~djurre/logs/N6_gmx461_verlet.log It would be great if you could point out some possible optimizations. >Note that with such a small system the scaling with the group scheme >surely becomes limited by imbalance and probably it won't scale much >further than 72 cores. At the same time, simulations with the verlet >scheme have shown scaling to below 100 atoms/core. I tried running on 84 cpus (56PP cores=400 atoms/PP core), but I did get an domain decomposition error. Maybe I could optimize -rcon and -dds further, however although the scaling to more CPUs is better with the verlet scheme, I think you will never win: with 72 CPUs Verlet is almost as fast as with group at 60 CPUs, however compared to 24 cpus the scaling per CPU is already down to 60%. But as Mark Abraham mentioned, it might be that my system is just to small to get the advantage of scaling that will be there in larger systems. Groetnis, Djurre -- 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
Thanks for your reply. In fact, I plan to study ion conduction through the peptide inserted in lipid membrane and acting as an ion channel. According to the literature, an ion across the membrane in less than 20 ns. Can I decide upon this information to apply pull code? You simulated the protofibril structures for 100 ns, in another article 25 ns. Ok, if there is not any universal recipe for it, what do you suggest me? Try and error? Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Friday, May 17, 2013 4:02 PM Subject: Re: [gmx-users] Re: Running Pull Code On 5/17/13 7:16 AM, Shima Arasteh wrote: > Thanks for your reply. > It' s around 5 nano seconds that I ran equilibration time on the system, and > the average pressure I see as a result, seems sensible. However I am not sure > if this criteria is sufficient? Others suggest to evaluate the box-dimension > changes using g_energy code to judge of sufficient equilibration time. > The box vectors won't tell you anything more than the pressure will since they're related quantities. The better question is, "What is a suitable starting structure for the system of interest?" The umbrella sampling tutorial (which everyone seems to take at literal face value as the only way to do things, which it is decidedly not) presents a simple, easy-to-understand method. In the paper I did (upon which I based the tutorial), I simulated the protofibril structures for 100 ns before I was confident they were suitably stable and representative of viable structures for doing SMD and US. Your mileage will vary and depends on the quality of the starting structure and what it is that you hope to determine. There is no magic recipe that is universal. -Justin > I appreciate your suggestion. > > > Sincerely, > Shima > > > - Original Message - > From: Thomas Schlesier > To: gmx-users@gromacs.org > Cc: > Sent: Friday, May 17, 2013 3:30 PM > Subject: [gmx-users] Re: Running Pull Code > > The three steps (EM, NVT and NPT) are to equilibrate the system. How > much time these steps need depends on the system. But i would assume a > ouple of nanosecounds are sufficient for most systems. You could look > into the literature, how long other people equilibrate systems which are > similar to ours. > If the system is equilibrated, you an start to perform the pulling > simulation to obtain the individual structure for the later umbrella > sampling. > > Greetings > Thomas > > Am 17.05.2013 07:46, schrieb gmx-users-requ...@gromacs.org: >> Hi, >> >> I have a system composed of POPC/peptide/water/ions. I aim to study ion >> conduction through the peptide using umbrella sampling. >> I built the system and ran EM, NVT, NPT successfully, but have not run md >> yet. I' d like to know if the system is required of passing a few >> nanoseconds md? Or I might be able to go to Umbrella Sampling straight after >> NPT? >> As I studied in Justin's tutorial, running pull code is done after some >> typical steps of every simulation ( EM, NVT, NPT). But I dont know if is >> correct generally for other systems as well? >> >> Would you please give me any suggestions? >> >> >> Thanks in advance. >> Sincerely, >> Shima? > -- 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] Comparing Gromacs versions
On Fri, May 17, 2013 at 2:21 PM, Djurre de Jong-Bruinink < djurredej...@yahoo.com> wrote: > >You are doing simulations with a lot of water (and perhaps with charge > groups), > > >and that is the case where an unbuffered group scheme has the best > performance. > > >How much you like the physics is another story. > > > Thank you for your answer. I didn't realize a system like this is already > in the "lot of water"-regime (it makes sense though, ~95% of the particles > is water). I could lower the water content a bit by reducing the solute to > box distance (eg from 1.5 to 1.2/1.0nm), but that only saves a few percent. > In practice it will mean that for any system containing soluble proteins, > the group scheme will still be faster? Right? > This was what the group kernels were built for. But after a certain number of cores (as Szilard said), by construction, the group scheme will stop scaling, and the group and verlet performance curves will certainly cross. The PME performance also starts to die at large MPI process counts because of the global inter-PME-node communication, which you can see in the .log file timing breakdowns. I expect you are not being fair to the Verlet scheme at high core counts by requiring high MPI process counts by turning off OpenMP. Mark > Groetnis, > Djurre de Jong > -- > 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
Re: [gmx-users] Re: Running Pull Code
Thanks for your reply. In fact, I plan to study ion conduction through the peptide inserted in lipid membrane and acting as an ion channel. According to the literature, an ion across the membrane in less than 20 ns. Can I decide upon this information to apply pull code? You simulated the protofibril structures for 100 ns, in another article 25 ns. Ok, if there is not any universal recipe for it, what do you suggest me? Try and error? Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Friday, May 17, 2013 4:02 PM Subject: Re: [gmx-users] Re: Running Pull Code On 5/17/13 7:16 AM, Shima Arasteh wrote: > Thanks for your reply. > It' s around 5 nano seconds that I ran equilibration time on the system, and > the average pressure I see as a result, seems sensible. However I am not sure > if this criteria is sufficient? Others suggest to evaluate the box-dimension > changes using g_energy code to judge of sufficient equilibration time. > The box vectors won't tell you anything more than the pressure will since they're related quantities. The better question is, "What is a suitable starting structure for the system of interest?" The umbrella sampling tutorial (which everyone seems to take at literal face value as the only way to do things, which it is decidedly not) presents a simple, easy-to-understand method. In the paper I did (upon which I based the tutorial), I simulated the protofibril structures for 100 ns before I was confident they were suitably stable and representative of viable structures for doing SMD and US. Your mileage will vary and depends on the quality of the starting structure and what it is that you hope to determine. There is no magic recipe that is universal. -Justin > I appreciate your suggestion. > > > Sincerely, > Shima > > > - Original Message - > From: Thomas Schlesier > To: gmx-users@gromacs.org > Cc: > Sent: Friday, May 17, 2013 3:30 PM > Subject: [gmx-users] Re: Running Pull Code > > The three steps (EM, NVT and NPT) are to equilibrate the system. How > much time these steps need depends on the system. But i would assume a > ouple of nanosecounds are sufficient for most systems. You could look > into the literature, how long other people equilibrate systems which are > similar to ours. > If the system is equilibrated, you an start to perform the pulling > simulation to obtain the individual structure for the later umbrella > sampling. > > Greetings > Thomas > > Am 17.05.2013 07:46, schrieb gmx-users-requ...@gromacs.org: >> Hi, >> >> I have a system composed of POPC/peptide/water/ions. I aim to study ion >> conduction through the peptide using umbrella sampling. >> I built the system and ran EM, NVT, NPT successfully, but have not run md >> yet. I' d like to know if the system is required of passing a few >> nanoseconds md? Or I might be able to go to Umbrella Sampling straight after >> NPT? >> As I studied in Justin's tutorial, running pull code is done after some >> typical steps of every simulation ( EM, NVT, NPT). But I dont know if is >> correct generally for other systems as well? >> >> Would you please give me any suggestions? >> >> >> Thanks in advance. >> Sincerely, >> Shima? > -- 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] Comparing Gromacs versions
>You are doing simulations with a lot of water (and perhaps with charge >groups), >and that is the case where an unbuffered group scheme has the best >performance. >How much you like the physics is another story. Thank you for your answer. I didn't realize a system like this is already in the "lot of water"-regime (it makes sense though, ~95% of the particles is water). I could lower the water content a bit by reducing the solute to box distance (eg from 1.5 to 1.2/1.0nm), but that only saves a few percent. In practice it will mean that for any system containing soluble proteins, the group scheme will still be faster? Right? Groetnis, Djurre de Jong -- 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] Inconsistent results in different clusters and cores
I am extremely sorry for spaming the mail box. It was quite unintentionally. Believe me I was getting the following error every time while sending the mail. Final-Recipient: rfc822; jaanus.k...@eesti.ee Action: failed Status: 5.0.0 Diagnostic-Code: X-Postfix; mail forwarding loop for jaanus.k...@eesti.ee Tarak -- Forwarded message -- From: tarak karmakar To: Discussion list for GROMACS users Cc: Date: Fri, 17 May 2013 15:50:25 +0530 Subject: Re: [gmx-users] Inconsistent results in different clusters and cores On Fri, May 17, 2013 at 5:36 PM, Mark Abraham wrote: > On Fri, May 17, 2013 at 1:23 PM, Justin Lemkul wrote: > >> >> >> On 5/17/13 6:20 AM, tarak karmakar wrote: >> >>> I have read the 'implementation of charmm in gromacs' by bjelkmar, >>> JCTC. There they have used following cut-offs >>> coulombtype=PME >>> rcoulomb=1.2 >>> vdwtype=switch >>> rvdw=1.2 >>> rvdw-switch=1.0 >>> >>> I am not sure about rlist. >>> >>> >> It's really unnecessary to spam the list with a dozen requests that ask >> the same question. >> >> By definition, with PME, rlist = rcoulomb. For CHARMM, use rlistlong = >> 1.4; the message that is printed below is an error that has been fixed in >> newer versions. > > > Are you sure? Looking at the logic in src/mdlib/read_ir.c, I could not see > how Tarak's input could have led (correctly) to that note from grompp. I am > thinking that > https://github.com/gromacs/gromacs/blob/release-4-5-patches/src/kernel/readir.c#L170 > is > setting rlistlong = rlist, and so > https://github.com/gromacs/gromacs/blob/release-4-5-patches/src/kernel/readir.c#L586 > gets > double-crossed. > > (Note that http://redmine.gromacs.org/issues/1164 pertained to a slightly > different issue.) > > 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 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] Comparing Gromacs versions
The answer is in the log files, in particular the performance summary should indicate where is the performance difference. If you post your log files somewhere we can probably give further tips on optimizing your run configurations. Note that with such a small system the scaling with the group scheme surely becomes limited by imbalance and probably it won't scale much further than 72 cores. At the same time, simulations with the verlet scheme have shown scaling to below 100 atoms/core. Cheers, -- Szilárd On Fri, May 17, 2013 at 11:07 AM, Djurre de Jong-Bruinink wrote: > Dear all, > > We recently did some comparisons of gmx 4.5.5, 4.6.1+group and 4.6.1+verlet > cutoff scheme. The system was a protein (amber99) in water (tip3p) in a > triclinic box (23k atoms total). We're using pme with a realspace > cutoff=0.9nm, gridspacing=0.12nm, npme=-1, which based on g_tune_pme gives > (close to) best performance. Below some performance measure (ns/day) from > 100,000 step runs: > > CPUs G455G461+group G461+verlet > 2434.9 43.1 35.3 > 3647.6 57.8 49.7 > 4850.8 65.9 60.4 > 6059.9 81.8 71.1 > 7257.7 78.7 78.2 > > The scaling to more CPUs in 4.6.1 is much better (thank you developers for > putting up all the hard work!), however I would have expected more > improvements from the verlet scheme. Note that both 455 and 461 have been > compiled with MPI only (no OMP, GPU), and 461 was compiled with gcc (4.7.2). > I did change the nstlist from 5 to 10 for the verlet scheme only. > > > Are these results expected given the setup? Is there anything I'm doing wrong? > > Thanks in advance, > Djurre de Jong > -- > 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
Re: [gmx-users] Inconsistent results in different clusters and cores
On Fri, May 17, 2013 at 1:23 PM, Justin Lemkul wrote: > > > On 5/17/13 6:20 AM, tarak karmakar wrote: > >> I have read the 'implementation of charmm in gromacs' by bjelkmar, >> JCTC. There they have used following cut-offs >> coulombtype=PME >> rcoulomb=1.2 >> vdwtype=switch >> rvdw=1.2 >> rvdw-switch=1.0 >> >> I am not sure about rlist. >> >> > It's really unnecessary to spam the list with a dozen requests that ask > the same question. > > By definition, with PME, rlist = rcoulomb. For CHARMM, use rlistlong = > 1.4; the message that is printed below is an error that has been fixed in > newer versions. Are you sure? Looking at the logic in src/mdlib/read_ir.c, I could not see how Tarak's input could have led (correctly) to that note from grompp. I am thinking that https://github.com/gromacs/gromacs/blob/release-4-5-patches/src/kernel/readir.c#L170 is setting rlistlong = rlist, and so https://github.com/gromacs/gromacs/blob/release-4-5-patches/src/kernel/readir.c#L586 gets double-crossed. (Note that http://redmine.gromacs.org/issues/1164 pertained to a slightly different issue.) 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] Re: REMD analysis
Well use a regular plotting software and look at it or do some more elaborated operation in or out the software to estimate the overlap :)) On May 17, 2013, at 1:14 PM, bharat gupta wrote: > Dear Sir, > > I ran the REMD simulation with temp. distribution discussed in my last > thread. Each replica was run for 50 ns > > Replica exchange statistics > Repl 24999 attempts, 12500 odd, 12499 even > Repl average probabilities: > Repl 0123456789 10 11 12 > Repl .22 .19 .18 .16 .19 .21 .23 .25 .26 .29 .28 .28 > Repl number of exchanges: > Repl 0123456789 10 11 12 > Repl 2661 2369 2296 2008 2360 2668 2866 3119 3234 3549 3469 3475 > Repl average number of exchanges: > Repl 0123456789 10 11 12 > Repl .21 .19 .18 .16 .19 .21 .23 .25 .26 .28 .28 .28 > > Now, how to find the potential energy overlap for each replica??.. I have > obtained the pot. energy for each replica separately.. > > -- > 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
Re: [gmx-users] Re: Running Pull Code
On 5/17/13 7:16 AM, Shima Arasteh wrote: Thanks for your reply. It' s around 5 nano seconds that I ran equilibration time on the system, and the average pressure I see as a result, seems sensible. However I am not sure if this criteria is sufficient? Others suggest to evaluate the box-dimension changes using g_energy code to judge of sufficient equilibration time. The box vectors won't tell you anything more than the pressure will since they're related quantities. The better question is, "What is a suitable starting structure for the system of interest?" The umbrella sampling tutorial (which everyone seems to take at literal face value as the only way to do things, which it is decidedly not) presents a simple, easy-to-understand method. In the paper I did (upon which I based the tutorial), I simulated the protofibril structures for 100 ns before I was confident they were suitably stable and representative of viable structures for doing SMD and US. Your mileage will vary and depends on the quality of the starting structure and what it is that you hope to determine. There is no magic recipe that is universal. -Justin I appreciate your suggestion. Sincerely, Shima - Original Message - From: Thomas Schlesier To: gmx-users@gromacs.org Cc: Sent: Friday, May 17, 2013 3:30 PM Subject: [gmx-users] Re: Running Pull Code The three steps (EM, NVT and NPT) are to equilibrate the system. How much time these steps need depends on the system. But i would assume a ouple of nanosecounds are sufficient for most systems. You could look into the literature, how long other people equilibrate systems which are similar to ours. If the system is equilibrated, you an start to perform the pulling simulation to obtain the individual structure for the later umbrella sampling. Greetings Thomas Am 17.05.2013 07:46, schrieb gmx-users-requ...@gromacs.org: Hi, I have a system composed of POPC/peptide/water/ions. I aim to study ion conduction through the peptide using umbrella sampling. I built the system and ran EM, NVT, NPT successfully, but have not run md yet. I' d like to know if the system is required of passing a few nanoseconds md? Or I might be able to go to Umbrella Sampling straight after NPT? As I studied in Justin's tutorial, running pull code is done after some typical steps of every simulation ( EM, NVT, NPT). But I dont know if is correct generally for other systems as well? Would you please give me any suggestions? Thanks in advance. Sincerely, Shima? -- 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] Inconsistent results in different clusters and cores
On 5/17/13 6:20 AM, tarak karmakar wrote: I have read the 'implementation of charmm in gromacs' by bjelkmar, JCTC. There they have used following cut-offs coulombtype=PME rcoulomb=1.2 vdwtype=switch rvdw=1.2 rvdw-switch=1.0 I am not sure about rlist. It's really unnecessary to spam the list with a dozen requests that ask the same question. By definition, with PME, rlist = rcoulomb. For CHARMM, use rlistlong = 1.4; the message that is printed below is an error that has been fixed in newer versions. -Justin On Fri, May 17, 2013 at 1:46 PM, tarak karmakar wrote: Now if I increase the rlist it is showing that With coulombtype = PME, rcoulomb must be equal to rlist If you want optimal energy conservation or exact integration use PME-Switch I don't know exactly what will be the best set up with charmm force field. Any suggestion please!! Thanks, Tarak On Fri, May 17, 2013 at 1:34 PM, tarak karmakar wrote: What about Dispersion Correction ? But if I use this set of informations ; 7.3.3 Run Control integrator = md; md integrator tinit = 0 ; [ps] starting time for run dt = 0.001 ; [ps] time step for integration nsteps = 500 ; maximum number of steps to integrate, 0.001 * 50,00,000 =5 ns nstcomm = 1 ; [steps] frequency of mass motion removal comm_grps = system; group(s) for center of mass motion removal comm_mode = linear ; 7.3.8 Output Control nstxout = 5000 ; [steps] freq to write coordinates to trajectory nstvout = 5000 ; [steps] freq to write velocities to trajectory nstfout = 5000 ; [steps] freq to write forces to trajectory nstlog = 1000 ; [steps] freq to write energies to log file nstenergy = 1000 ; [steps] freq to write energies to energy file nstxtcout = 1000 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 1000 ; [real] precision to write xtc trajectory xtc_grps= System; group(s) to write to xtc trajectory energygrps = protein ligand ; 7.3.9 Neighbor Searching nstlist = 10; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list rlistlong = 1.4 ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off fourierspacing = 0.16 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.11 VdW vdwtype = switch; twin-range cut-off with rlist where rvdw >= rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw-switch = 1.0 DispCorr= Ener ; apply long range dispersion corrections for energy ; 7.3.14 Temperature Coupling tcoupl = nose-hoover ; temperature coupling tc_grps = system; groups to couple seperately to temperature bath tau_t = 1.0 ; [ps] time constant for coupling ref_t = 300 ; [K] reference temperature for coupling ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman ; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 1.0 ; [ps] time constant for coupling compressibility = 4.5e-5; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling gen_vel = yes ; velocity generation gen_temp= 300 gen_seed= 8877691 ; 7.3.18 Bonds constraints = h-bonds ; covalent h-bonds constraints constraint_algorithm= LINCS ; LINear Constraint Solver continuation= yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain It is showing
[gmx-users] Re: REMD analysis
Dear Sir, I ran the REMD simulation with temp. distribution discussed in my last thread. Each replica was run for 50 ns Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 Repl .22 .19 .18 .16 .19 .21 .23 .25 .26 .29 .28 .28 Repl number of exchanges: Repl 0123456789 10 11 12 Repl 2661 2369 2296 2008 2360 2668 2866 3119 3234 3549 3469 3475 Repl average number of exchanges: Repl 0123456789 10 11 12 Repl .21 .19 .18 .16 .19 .21 .23 .25 .26 .28 .28 .28 Now, how to find the potential energy overlap for each replica??.. I have obtained the pot. energy for each replica separately.. -- 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
Re: [gmx-users] Re: Running Pull Code
Thanks for your reply. It' s around 5 nano seconds that I ran equilibration time on the system, and the average pressure I see as a result, seems sensible. However I am not sure if this criteria is sufficient? Others suggest to evaluate the box-dimension changes using g_energy code to judge of sufficient equilibration time. I appreciate your suggestion. Sincerely, Shima - Original Message - From: Thomas Schlesier To: gmx-users@gromacs.org Cc: Sent: Friday, May 17, 2013 3:30 PM Subject: [gmx-users] Re: Running Pull Code The three steps (EM, NVT and NPT) are to equilibrate the system. How much time these steps need depends on the system. But i would assume a ouple of nanosecounds are sufficient for most systems. You could look into the literature, how long other people equilibrate systems which are similar to ours. If the system is equilibrated, you an start to perform the pulling simulation to obtain the individual structure for the later umbrella sampling. Greetings Thomas Am 17.05.2013 07:46, schrieb gmx-users-requ...@gromacs.org: > Hi, > > I have a system composed of POPC/peptide/water/ions. I aim to study ion > conduction through the peptide using umbrella sampling. > I built the system and ran EM, NVT, NPT successfully, but have not run md > yet. I' d like to know if the system is required of passing a few nanoseconds > md? Or I might be able to go to Umbrella Sampling straight after NPT? > As I studied in Justin's tutorial, running pull code is done after some > typical steps of every simulation ( EM, NVT, NPT). But I dont know if is > correct generally for other systems as well? > > Would you please give me any suggestions? > > > Thanks in advance. > Sincerely, > Shima? -- 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] Comparing Gromacs versions
On Fri, May 17, 2013 at 11:07 AM, Djurre de Jong-Bruinink < djurredej...@yahoo.com> wrote: > Dear all, > > We recently did some comparisons of gmx 4.5.5, 4.6.1+group and > 4.6.1+verlet cutoff scheme. The system was a protein (amber99) in water > (tip3p) in a triclinic box (23k atoms total). We're using pme with a > realspace cutoff=0.9nm, gridspacing=0.12nm, npme=-1, which based on > g_tune_pme gives (close to) best performance. Below some performance > measure (ns/day) from 100,000 step runs: > > CPUs G455G461+group G461+verlet > 2434.9 43.1 35.3 > 3647.6 57.8 49.7 > 4850.8 65.9 60.4 > 6059.9 81.8 71.1 > 7257.7 78.7 78.2 > > The scaling to more CPUs in 4.6.1 is much better (thank you developers for > putting up all the hard work!), however I would have expected more > improvements from the verlet scheme. You are doing simulations with a lot of water (and perhaps with charge groups), and that is the case where an unbuffered group scheme has the best performance. How much you like the physics is another story. See http://www.gromacs.org/Documentation/Acceleration_and_parallelization and http://www.gromacs.org/Documentation/Cut-off_schemes Note that both 455 and 461 have been compiled with MPI only (no OMP, GPU), > and 461 was compiled with gcc (4.7.2). I did change the nstlist from 5 to > 10 for the verlet scheme only. > > > Are these results expected given the setup? Is there anything I'm doing > wrong? > I am not aware of a case where compiling without OpenMP is necessary/desirable for maximum performance. Whether you should use it (and how many OpenMP threads to use) depends on lots of things, particularly including what hardware you use and the atoms/core. You should experiment if you want maximum performance. Mark > Thanks in advance, > Djurre de Jong > -- > 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] Re: Running Pull Code
The three steps (EM, NVT and NPT) are to equilibrate the system. How much time these steps need depends on the system. But i would assume a ouple of nanosecounds are sufficient for most systems. You could look into the literature, how long other people equilibrate systems which are similar to ours. If the system is equilibrated, you an start to perform the pulling simulation to obtain the individual structure for the later umbrella sampling. Greetings Thomas Am 17.05.2013 07:46, schrieb gmx-users-requ...@gromacs.org: Hi, I have a system composed of POPC/peptide/water/ions. I aim to study ion conduction through the peptide using umbrella sampling. I built the system and ran EM, NVT, NPT successfully, but have not run md yet. I' d like to know if the system is required of passing a few nanoseconds md? Or I might be able to go to Umbrella Sampling straight after NPT? As I studied in Justin's tutorial, running pull code is done after some typical steps of every simulation ( EM, NVT, NPT). But I dont know if is correct generally for other systems as well? Would you please give me any suggestions? Thanks in advance. 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
Re: [gmx-users] Inconsistent results in different clusters and cores
I have read the 'implementation of charmm in gromacs' by bjelkmar, JCTC. There they have used following cut-offs coulombtype=PME rcoulomb=1.2 vdwtype=switch rvdw=1.2 rvdw-switch=1.0 I am not sure about rlist. Regards, Tarak On Fri, May 17, 2013 at 1:46 PM, tarak karmakar wrote: > Now if I increase the rlist it is showing that > > With coulombtype = PME, rcoulomb must be equal to rlist > If you want optimal energy conservation or exact integration > use PME-Switch > > I don't know exactly what will be the best set up with charmm force field. > > Any suggestion please!! > > Thanks, > > Tarak > > > > > On Fri, May 17, 2013 at 1:34 PM, tarak karmakar > wrote: >> >> What about Dispersion Correction ? >> But if I use this set of informations >> >> ; 7.3.3 Run Control >> integrator = md; md integrator >> tinit = 0 ; [ps] starting time for >> run >> dt = 0.001 ; [ps] time step for >> integration >> nsteps = 500 ; maximum number of steps >> to integrate, 0.001 * 50,00,000 =5 ns >> nstcomm = 1 ; [steps] frequency of >> mass motion removal >> comm_grps = system; group(s) for center of >> mass motion removal >> >> comm_mode = linear >> >> >> ; 7.3.8 Output Control >> nstxout = 5000 ; [steps] freq to write coordinates >> to trajectory >> nstvout = 5000 ; [steps] freq to write velocities to >> trajectory >> nstfout = 5000 ; [steps] freq to write forces to >> trajectory >> nstlog = 1000 ; [steps] freq to write energies >> to log file >> nstenergy = 1000 ; [steps] freq to write energies >> to energy file >> nstxtcout = 1000 ; [steps] freq to write >> coordinates to xtc trajectory >> xtc_precision = 1000 ; [real] precision to write xtc >> trajectory >> xtc_grps= System; group(s) to write to xtc >> trajectory >> energygrps = protein ligand >> >> ; 7.3.9 Neighbor Searching >> nstlist = 10; [steps] freq to update neighbor >> list >> ns_type = grid ; method of updating neighbor list >> pbc = xyz ; periodic boundary conditions in >> all directions >> rlist = 1.2 ; [nm] cut-off distance for the >> short-range neighbor list >> rlistlong = 1.4 >> >> ; 7.3.10 Electrostatics >> coulombtype = PME ; Particle-Mesh Ewald >> electrostatics >> rcoulomb= 1.2 ; [nm] distance for Coulomb >> cut-off >> fourierspacing = 0.16 ; [nm] grid spacing for FFT grid >> when using PME >> pme_order = 4 ; interpolation order for PME, 4 = >> cubic >> ewald_rtol = 1e-5 ; relative strength of >> Ewald-shifted potential at rcoulomb >> >> ; 7.3.11 VdW >> vdwtype = switch; twin-range cut-off with rlist >> where rvdw >= rlist >> rvdw= 1.2 ; [nm] distance for LJ cut-off >> rvdw-switch = 1.0 >> >> DispCorr= Ener ; apply long range dispersion >> corrections for energy >> >> >> ; 7.3.14 Temperature Coupling >> tcoupl = nose-hoover ; temperature coupling >> tc_grps = system; groups to couple seperately to >> temperature bath >> tau_t = 1.0 ; [ps] time constant for coupling >> ref_t = 300 ; [K] reference temperature for >> coupling >> >> ; 7.3.15 Pressure Coupling >> pcoupl = parrinello-rahman ; pressure coupling where >> box vectors are variable >> pcoupltype = isotropic ; pressure coupling in >> x-y-z directions >> tau_p = 1.0 ; [ps] time constant for >> coupling >> compressibility = 4.5e-5; [bar^-1] compressibility >> ref_p = 1.0 ; [bar] reference pressure >> for coupling >> >> gen_vel = yes ; velocity generation >> >> gen_temp= 300 >> gen_seed= 8877691 >> >> ; 7.3.18 Bonds >> constraints = h-bonds ; covalent h-bonds constraints >> constraint_algorithm= LINCS ; LINear Constraint Solver >> continuation= yes ; apply constraints to the start >> configuration >> lincs_order = 4 ; highest order in the expansion >> of the contraint coupling matrix >> lincs_iter = 1 ; number of iterations to correct >> for rotational lengthening >> lincs_warnangle = 30; [degrees] maximum angle that a >> bond can rotate before LINCS w
[gmx-users] cut-offs
Dear All, I have read the 'implementation of charmm in gromacs' by bjelkmar, JCTC. There they have used following cut-offs coulombtype=PME rcoulomb=1.2 vdwtype=switch rvdw=1.2 rvdw-switch=1.0 If I use the same numbers with rlist=1.2 it is showing warning saying rlist should be at lear 0.1 - 0.3 nm larger to get proper conservation of energy. Now, changing the rlist enforces to change the rcoulomb. Can anyone please suggest the best possible combination of these numbers? Thanks, 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] CHARMM lipid parameters
Dear all, How can I generate a particular lipid itp file compatible with CHARMM27 (say Cholesteryl oleate). The link for CHARMM compatible cholesterol parameters in the lipidbook website is also dead. Thanks a lot -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] (no subject)
Sir, I want to do pulling simulations for membrane protein and gold nanoparticles. Can you please suggest me some tutorials for calculating youngs modules ,stress and strain. 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] pulling simulations
Sir, I want to do pulling simulations for membrane protein and gold nanoparticles. Can you please suggest me some tutorials. 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] puuling simulations
http://www.gromacs.org/Documentation/Tutorials Sincerely, Shima - Original Message - From: Sathish Kumar To: Discussion list for GROMACS users Cc: Sent: Friday, May 17, 2013 2:08 PM Subject: [gmx-users] puuling simulations Sir, I want to do pulling simulations for membrane protein and gold nanoparticles. Can you please suggest me some tutorials. Thank You -- regards M.SathishKumar -- 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
[gmx-users] Fwd: puuling simulations
Sir, I want to do pulling simulations for membrane protein and gold nanoparticles. Can you please suggest me some tutorials. Thank You -- regards M.SathishKumar -- 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] puuling simulations
Sir, I want to do pulling simulations for membrane protein and gold nanoparticles. Can you please suggest me some tutorials. 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] charmm in gromacs cut-offs
Dear All, I'm using charmm force field for simulation of a protein ligand system. I have read the paper "implementation of charmm in gromacs by Bjelkmar, JCTC' They have used the following set up coulombtype = PME rcoulomb= 1.2 vdwtype = switch rvdw= 1.2 rvdw-switch = 1.0 Now, with this same set up if I use rlist = 1.2 rlistlong =1.4 It is showing the following warning "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw." Now, if I try to increase the rlist as rlist =1.3 Coulomb part is showing warning as "With coulombtype = PME, rcoulomb must be equal to rlist** If you want optimal energy conservation or exact integration use** PME-Switch*" I read few posts in this issue But the point, if I use rlist=rvdw then the dynamics will not be proper as in the neighbor list updating and energy calculations. Now, the any kind of change in the rlist essentially enforcing to change the coul cut-off. So, rlist and coul-cut-off are not independent of each other. Can any one suggest me the best possible use of these parameters? I am using gromacs-4.5.5 for simulations. Thanks, 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] Cholesteryl oleate parameters for CHARMM27 ff in Gromacs
Dear all, How can I generate a particular lipid itp file compatible with CHARMM27 (say Cholesteryl oleate). The link for CHARMM compatible cholesterol parameters in *lipidbook *website is also dead. Thanks a lot -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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, I'm using charmm force field for simulation of a protein ligand system. I have read the paper "implementation of charmm in gromacs by Bjelkmar, JCTC' They have used the following set up coulombtype = PME rcoulomb= 1.2 vdwtype = switch rvdw= 1.2 rvdw-switch = 1.0 Now, with this same set up if I use rlist = 1.2 rlistlong =1.4 It is showing the following warning "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw." Now, if I try to increase the rlist as rlist =1.3 Coulomb part is showing warning as "With coulombtype = PME, rcoulomb must be equal to rlist** If you want optimal energy conservation or exact integration use** PME-Switch*" I read few posts in this issue But the point, if I use rlist=rvdw then the dynamics will not be proper as in the neighbor list updating and energy calculations. Now, the any kind of change in the rlist essentially enforcing to change the coul cut-off. So, rlist and coul-cut-off are not independent of each other. Can any one suggest me the best possible use of these parameters? I am using gromacs-4.5.5 for simulations. Thanks, 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] charmm in gromacs cut-offs
Dear All, I'm using charmm force field for simulation of a protein ligand system. I have read the paper "implementation of charmm in gromacs by Bjelkmar, JCTC' They have used the following set up coulombtype = PME rcoulomb= 1.2 vdwtype = switch rvdw= 1.2 rvdw-switch = 1.0 Now, with this same set up if I use rlist = 1.2 rlistlong =1.4 It is showing the following warning "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw." Now, if I try to increase the rlist as rlist =1.3 Coulomb part is showing warning as "With coulombtype = PME, rcoulomb must be equal to rlist** If you want optimal energy conservation or exact integration use** PME-Switch*" I came across this post in the mailing list http://lists.gromacs.org/pipermail/gmx-users/2013-February/079037.html But the point, if I use rlist=rvdw then the dynamics will not be proper as in the neighbor list updating and energy calculations. Can any one suggest me the best possible use of these parameters? I am using gromacs-4.5.5 for simulations. Thanks, 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] charmm in gromacs cut-offs
Dear All, I'm using charmm force field for simulation of a protein ligand system. I have read the paper "implementation of charmm in gromacs by Bjelkmar, JCTC' They have used the following set up coulombtype = PME rcoulomb= 1.2 vdwtype = switch rvdw= 1.2 rvdw-switch = 1.0 Now, with this same set up if I use rlist = 1.2 rlistlong =1.4 It is showing the following warning "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw." Now, if I try to increase the rlist as rlist =1.3 Coulomb part is showing warning as "With coulombtype = PME, rcoulomb must be equal to rlist** If you want optimal energy conservation or exact integration use** PME-Switch*" I came across this post in the mailing list http://lists.gromacs.org/pipermail/gmx-users/2013-February/079037.html But the point, if I use rlist=rvdw then the dynamics will not be proper as in the neighbor list updating and energy calculations. Can any one suggest me the best possible use of these parameters? I am using gromacs-4.5.5 for simulations. Thanks, 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] Comparing Gromacs versions
Dear all, We recently did some comparisons of gmx 4.5.5, 4.6.1+group and 4.6.1+verlet cutoff scheme. The system was a protein (amber99) in water (tip3p) in a triclinic box (23k atoms total). We're using pme with a realspace cutoff=0.9nm, gridspacing=0.12nm, npme=-1, which based on g_tune_pme gives (close to) best performance. Below some performance measure (ns/day) from 100,000 step runs: CPUs G455 G461+group G461+verlet 24 34.9 43.1 35.3 36 47.6 57.8 49.7 48 50.8 65.9 60.4 60 59.9 81.8 71.1 72 57.7 78.7 78.2 The scaling to more CPUs in 4.6.1 is much better (thank you developers for putting up all the hard work!), however I would have expected more improvements from the verlet scheme. Note that both 455 and 461 have been compiled with MPI only (no OMP, GPU), and 461 was compiled with gcc (4.7.2). I did change the nstlist from 5 to 10 for the verlet scheme only. Are these results expected given the setup? Is there anything I'm doing wrong? Thanks in advance, Djurre de Jong -- 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, I'm using charmm force field for simulation of a protein ligand system. I have read the paper "implementation of charmm in gromacs by Bjelkmar, JCTC' They have used the following set up coulombtype = PME rcoulomb= 1.2 vdwtype = switch rvdw= 1.2 rvdw-switch = 1.0 Now, with this same set up if I use rlist = 1.2 rlistlong =1.4 It is showing the following warning NOTE 1 [file 02md.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. Now, if I try to increase the rlist as rlist =1.3 Coulomb part is showing warning as *ERROR 1 [file 02md.mdp]:**With coulombtype = PME, rcoulomb must be equal to rlist** If you want optimal energy conservation or exact integration use** PME-Switch* I came across this post in the mailing list http://lists.gromacs.org/pipermail/gmx-users/2013-February/079037.html But the point, if I use rlist=rvdw then the dynamics will not be proper as in the neighbor list updating and energy calculations. Can any one suggest me the best possible use of these parameters? I am using gromacs-4.5.5 for simulations. Thanks, 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] charmm in gromacs cut-offs
Dear All, I'm using charmm force field for simulation of a protein ligand system. I have read the paper "implementation of charmm in gromacs by Bjelkmar, JCTC' They have used the following set up coulombtype = PME rcoulomb= 1.2 vdwtype = switch rvdw= 1.2 rvdw-switch = 1.0 Now, with this same set up if I use rlist = 1.2 rlistlong =1.4 It is showing the following warning NOTE 1 [file 02md.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. Now, if I try to increase the rlist as rlist =1.3 Coulomb part is showing warning as *ERROR 1 [file 02md.mdp]:**With coulombtype = PME, rcoulomb must be equal to rlist** If you want optimal energy conservation or exact integration use** PME-Switch* I came across this post in the mailing list http://lists.gromacs.org/pipermail/gmx-users/2013-February/079037.html But the point, if I use rlist=rvdw then the dynamics will not be proper as in the neighbor list updating and energy calculations. Can any one suggest me the best possible use of these parameters? I am using gromacs-4.5.5 for simulations. Thanks, 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
Re: [gmx-users] 1-4 scaling factor
See chapter 5 Mark On May 17, 2013 8:25 AM, "tarak karmakar" wrote: > Dear All, > > How do I incorporate the 1-4 scaling factor ( e.g., 1.0 for CHARMM and > 0.833 in AMBER) in gromacs? Or, is it internally taken care of by gromacs > while specifying the -ff flag? > > NAMD input file uses the following keyword > > 1-4scaling 1.0 (for charmm force field) > > > Thanks, > 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 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] Reduced Units
I don't understand what you are asking for. Mark On May 17, 2013 7:59 AM, "Rasoul Nasiri" wrote: > Are you sure lattice cell set up in f.c.c structure has been explained > there for the positions of molecules? > > > > > On Thu, May 16, 2013 at 3:28 PM, Mark Abraham >wrote: > > > Does manual 2.3 help? > > > > > > On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri > > wrote: > > > > > Hi All, > > > > > > Has anyone performed MD simulation on fluids in reduced units with > > GROMACS? > > > I just wandering how the obtained density values through the box should > > be > > > converted in the SI unit (Kg/m3). > > > > > > Thanks > > > Rasoul > > > -- > > > 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://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] Inconsistent results in different clusters and cores
Now if I increase the rlist it is showing that With coulombtype = PME, rcoulomb must be equal to rlist If you want optimal energy conservation or exact integration use PME-Switch I don't know exactly what will be the best set up with charmm force field. Any suggestion please!! Thanks, Tarak On Fri, May 17, 2013 at 1:34 PM, tarak karmakar wrote: > What about Dispersion Correction ? > But if I use this set of informations > > ; 7.3.3 Run Control > integrator = md; md integrator > tinit = 0 ; [ps] starting time for > run > dt = 0.001 ; [ps] time step for > integration > nsteps = 500 ; maximum number of steps > to integrate, 0.001 * 50,00,000 =5 ns > nstcomm = 1 ; [steps] frequency of > mass motion removal > comm_grps = system; group(s) for center of > mass motion removal > > comm_mode = linear > > > ; 7.3.8 Output Control > nstxout = 5000 ; [steps] freq to write coordinates > to trajectory > nstvout = 5000 ; [steps] freq to write velocities to > trajectory > nstfout = 5000 ; [steps] freq to write forces to > trajectory > nstlog = 1000 ; [steps] freq to write energies > to log file > nstenergy = 1000 ; [steps] freq to write energies > to energy file > nstxtcout = 1000 ; [steps] freq to write > coordinates to xtc trajectory > xtc_precision = 1000 ; [real] precision to write xtc > trajectory > xtc_grps= System; group(s) to write to xtc > trajectory > energygrps = protein ligand > > ; 7.3.9 Neighbor Searching > nstlist = 10; [steps] freq to update neighbor > list > ns_type = grid ; method of updating neighbor list > pbc = xyz ; periodic boundary conditions in > all directions > rlist = 1.2 ; [nm] cut-off distance for the > short-range neighbor list > rlistlong = 1.4 > > ; 7.3.10 Electrostatics > coulombtype = PME ; Particle-Mesh Ewald > electrostatics > rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off > fourierspacing = 0.16 ; [nm] grid spacing for FFT grid > when using PME > pme_order = 4 ; interpolation order for PME, 4 = > cubic > ewald_rtol = 1e-5 ; relative strength of > Ewald-shifted potential at rcoulomb > > ; 7.3.11 VdW > vdwtype = switch; twin-range cut-off with rlist > where rvdw >= rlist > rvdw= 1.2 ; [nm] distance for LJ cut-off > rvdw-switch = 1.0 > > DispCorr= Ener ; apply long range dispersion > corrections for energy > > > ; 7.3.14 Temperature Coupling > tcoupl = nose-hoover ; temperature coupling > tc_grps = system; groups to couple seperately to > temperature bath > tau_t = 1.0 ; [ps] time constant for coupling > ref_t = 300 ; [K] reference temperature for > coupling > > ; 7.3.15 Pressure Coupling > pcoupl = parrinello-rahman ; pressure coupling where > box vectors are variable > pcoupltype = isotropic ; pressure coupling in > x-y-z directions > tau_p = 1.0 ; [ps] time constant for > coupling > compressibility = 4.5e-5; [bar^-1] compressibility > ref_p = 1.0 ; [bar] reference pressure > for coupling > > gen_vel = yes ; velocity generation > > gen_temp= 300 > gen_seed= 8877691 > > ; 7.3.18 Bonds > constraints = h-bonds ; covalent h-bonds constraints > constraint_algorithm= LINCS ; LINear Constraint Solver > continuation= yes ; apply constraints to the start > configuration > lincs_order = 4 ; highest order in the expansion > of the contraint coupling matrix > lincs_iter = 1 ; number of iterations to correct > for rotational lengthening > lincs_warnangle = 30; [degrees] maximum angle that a > bond can rotate before LINCS will complain > > > It is showing the following warning > > "For energy conservation with switch/shift potentials, rlist should be 0.1 > to 0.3 nm larger than rvdw." > > > > > > > On Sun, May 12, 2013 at 11:57 PM, tarak karmakar wrote: > >> Oh ! >> Thanks a lot Justin. I'll rerun all my jobs with this corrected mdp. >> Restrains things I didn't follow properly, anyway I'll read about this. >> >> >> On Sun, May 12, 2013
Re: [gmx-users] Inconsistent results in different clusters and cores
What about Dispersion Correction ? But if I use this set of informations ; 7.3.3 Run Control integrator = md; md integrator tinit = 0 ; [ps] starting time for run dt = 0.001 ; [ps] time step for integration nsteps = 500 ; maximum number of steps to integrate, 0.001 * 50,00,000 =5 ns nstcomm = 1 ; [steps] frequency of mass motion removal comm_grps = system; group(s) for center of mass motion removal comm_mode = linear ; 7.3.8 Output Control nstxout = 5000 ; [steps] freq to write coordinates to trajectory nstvout = 5000 ; [steps] freq to write velocities to trajectory nstfout = 5000 ; [steps] freq to write forces to trajectory nstlog = 1000 ; [steps] freq to write energies to log file nstenergy = 1000 ; [steps] freq to write energies to energy file nstxtcout = 1000 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 1000 ; [real] precision to write xtc trajectory xtc_grps= System; group(s) to write to xtc trajectory energygrps = protein ligand ; 7.3.9 Neighbor Searching nstlist = 10; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list rlistlong = 1.4 ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off fourierspacing = 0.16 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.11 VdW vdwtype = switch; twin-range cut-off with rlist where rvdw >= rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw-switch = 1.0 DispCorr= Ener ; apply long range dispersion corrections for energy ; 7.3.14 Temperature Coupling tcoupl = nose-hoover ; temperature coupling tc_grps = system; groups to couple seperately to temperature bath tau_t = 1.0 ; [ps] time constant for coupling ref_t = 300 ; [K] reference temperature for coupling ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman ; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 1.0 ; [ps] time constant for coupling compressibility = 4.5e-5; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling gen_vel = yes ; velocity generation gen_temp= 300 gen_seed= 8877691 ; 7.3.18 Bonds constraints = h-bonds ; covalent h-bonds constraints constraint_algorithm= LINCS ; LINear Constraint Solver continuation= yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain It is showing the following warning "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw." On Sun, May 12, 2013 at 11:57 PM, tarak karmakar wrote: > Oh ! > Thanks a lot Justin. I'll rerun all my jobs with this corrected mdp. > Restrains things I didn't follow properly, anyway I'll read about this. > > > On Sun, May 12, 2013 at 11:27 PM, Justin Lemkul wrote: > >> >> >> On 5/12/13 1:53 PM, tarak karmakar wrote: >> >>> Thanks, >>> >>> I have used CGENFF force field parameters for the ligand generated from >>> PARMCHEM with 0 penalties. For protein I have used CHARMM36 force field. >>> my npt.mdp file is as follows, >>> >>> ; 7.3.3 Run Control >>> integrator = md >>> >> >> Bug 1021 was only relevant with md-vv, so it is not your problem here. >> >> >> tinit = 0 >>> dt = 0.001 >>> nsteps = 500 >>> nstcomm = 1
Re: [gmx-users] Hydrogen Bond analysis using Gromacs
HI,
s0, s1,… is (xm)grace codes that refer to the different datasets in the file.
Gromacs prints the datasets as different columns. I suggest opening the file
with xmgrace -nxy yourxvgfile.xvg. As for the -life option, the results are
based on a too wimple kinetic model for most applications.
Erik
On 17 May 2013, at 08:21, Keerthana S.P Periasamy
wrote:
>
>
> Hai
> In Hydrogen Bonding Analysis, I want to know about the the
> interpretation of option -life and -ac (autocorrelation) I cannot
> understand what the columns P(t) and t p(t) describe and how to interpret
> this. Similarly after tagging -ac option in .xvg file I am getting@ s0
> legend "Ac\sfin sys\v{}\z{}(t)"
> @ s1 legend "Ac(t)"
> @ s2 legend "Cc\scontact,hb\v{}\z{}(t)" @ s3 legend "-dAc\sfs\v{}\z{}/dt"
> i also want to know what these s0 to s3 specify and how to interpret
> this.Please help me to get cleared of my doubts so that I can continue
> further. Thanks in Advance
> with regardsKeerthanaPeriasamy
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
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--
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