Re: [gmx-users] problem: gromacs run on gpu
Can you try to open the script in vi, delete the mdrun line and then manually retype it? On 7/12/2017 11:03 PM, leila karami wrote: Dear Gromacs users, I am doing md simulation on Gromacs 5.1.3. on GPU in Rocks cluster system using command: gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on All things are ok. When I use this command in a script to do md simulation by queuing system: - #!/bin/bash #$ -S /bin/bash #$ -q gpu.q #$ -cwd #$ -N cell_1 #$ -e error_1.dat #$ -o output_1.dat echo "Job started at date" gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on echo "Job Ended at date" - I encountered with following error: Program: gmx mdrun, VERSION 5.1.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234) Function:void gmx::CommandLineParser::parse(int*, char**) Error in user input: Invalid command-line options In command-line option -pin Invalid value: on For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Halting program gmx mdrun -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. --- How to resolve this error? Any help will be highly appreciated -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] problem: gromacs run on gpu
Dear Gromacs users, I am doing md simulation on Gromacs 5.1.3. on GPU in Rocks cluster system using command: gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on All things are ok. When I use this command in a script to do md simulation by queuing system: - #!/bin/bash #$ -S /bin/bash #$ -q gpu.q #$ -cwd #$ -N cell_1 #$ -e error_1.dat #$ -o output_1.dat echo "Job started at date" gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on echo "Job Ended at date" - I encountered with following error: Program: gmx mdrun, VERSION 5.1.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234) Function:void gmx::CommandLineParser::parse(int*, char**) Error in user input: Invalid command-line options In command-line option -pin Invalid value: on For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Halting program gmx mdrun -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. --- How to resolve this error? Any help will be highly appreciated -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error
I wonder if the "couple-intramol = yes" is a must. Does it have any influence on the output results if we turn off the intra-molecular non-bonded interactions of a large infinite molecule? The answer to your question has nothing to do with Gromacs, but with understanding the difference between crystals and biomolecules (for which Gromacs was designed). Also (unrelated), it is a common misconception to believe that PBC makes something infinite -- the effective size of your system is entirely determined by the supercell size (proof: consider the ripples in hBN and determine the lowest wavelength of the ripple that can propagate -- it is commensurate with the box size). In an infinite system, you can have an immensely long wave (though not infinite, as shown by Landau a while back). PBC does not make anything infinite, it is a mathematical way of avoiding surfaces. There is no universal force field for HBN, so I am using a modified gromos54a7_atb force field, i.e., manually adding the parameters for boron and nitrogen to the bonded & nonbonded .itp files. Oh, I know that there is no force fields for these structures. ;) My question was about which Gromacs ff you were using to insert your parameters, and, most importantly, where those parameters came from. The parameters are obtained from literature. What literature? All bio-style ff adaptations of solid-state potentials (e.g. Tersoff-Brenner for hBN) I am aware of make it very clear that "intramolecular" interactions between atoms sharing up to a fairly distant covalently bound neighbor are limited to bonds and angles. This comes from the math involved in developing potentials for crystals. There was a recent question regarding this very problem here, which was solved by setting a larger nrexcl value. In your case, you solved it with turning off intramolecular coupling. In fact, if you set your nrexcl to something like 4 or 5, you may not even need to turn off the coupling. But then again, I don't know where the parameters came from. Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error
Hi Alex, Thank you for your reply. Here below is my response to your comments. hBN is hardly a common subject of simulation for Gromacs folks, but let's see... 1. When you run the simulation in vacuum, do you get the same error? Does a 300K vacuum simulation result in reasonable sheet behavior? What about NVT? The answer is yes. I ran more tests today, and I think I have found exactly how the error came out. In fact, if I remove the whole free energy calculation section from my mdp file, the system will run perfectly in parallel, both HBN in vacuum and HBN in solution. So I suspect somewhere in FEC section is causing the trouble. Then I looked up each command in GROMACS documentation, and found this "couple-intramol" flag: "couple-intramol: no All intra-molecular non-bonded interactions for moleculetype couple-moltype are replaced by exclusions and explicit pair interactions. In this manner the decoupled state of the molecule corresponds to the proper vacuum state without periodicity effects. yes The intra-molecular Van der Waals and Coulomb interactions are also turned on/off. This can be useful for partitioning free-energies of relatively large molecules, where the intra-molecular non-bonded interactions might lead to kinetically trapped vacuum conformations. The 1-4 pair interactions are not turned off." I wonder if the "couple-intramol = no" works periodic molecules. In my mdp file, I set the flag to "no", because both reference tutorials set it to "no". However, I am dealing with a relative large molecule with periodicity, so I should have set this flag to "yes". Then I ran several more test with "couple-intramol = yes". Now, for EM/NVT/NPT/PROD_MD, the system could finally run in parallel. No more disturbing errors. Hooray!! But I am still confused about the setting of "couple-intramol". Why it can run parallelly if "couple-intramol" is set "yes". The hBN sheet in my simulation is infinite with PBC. I wonder if the "couple-intramol = yes" is a must. Does it have any influence on the output results if we turn off the intra-molecular non-bonded interactions of a large infinite molecule? Please note that "periodic-molecules = yes" in all my simulations. 2. What GROMACS forcefield are you using and what are the nonbonded types for boron and nitrogen? There is no universal force field for HBN, so I am using a modified gromos54a7_atb force field, i.e., manually adding the parameters for boron and nitrogen to the bonded & nonbonded .itp files. The parameters are obtained from literature. 3. How was the topology obtained? If x2top was used, was the BN sample in a box with in-plane PBC? I did use x2top to generate the topology of hBN sheet by using the following command: g_x2top_mpi -f HBN-z-2.gro -o hbn-x2top.top -ff bnt_oplsaa -name BNT -noparam -pbc -alldih PBC is considered here. And some additional modifications are carried out manually. Best, Xuliang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx select
Hi, Can you please copy, paste and post your actual commands. I don't think your use of quote marks would have led to a valid shell command. The whole selection text will need to be inside some quotes. Mark On Wed, 12 Jul 2017 23:47 Pandya, Akashwrote: > I have used the same name in my coordinate file. For Glycine it is spelt > as Glyci, so the word has been cut off. I know this is correct because I > use the same name in VMD. > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 12 July 2017 22:42 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] gmx select > > Hi, > > What are the residue names in your coordinate file? Glyci probably doesn't > fit > > Mark > > On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash > wrote: > > > Hi all, > > > > > > I am trying to select all the glycine molecules with 0.5nm of my protein. > > I tried both of these commands I got from the gromacs website: > > > > gmx select -f output.gro -select "Close to protein" resname Glyci and > > within 0.5 of group "Protein"' -ofpdb > > > > gmx select -f output.xtc -s output.tpr (my converted input file) > > -select "Close to protein" resname Glyci and within 0.5 of group > > "Protein"' -ofpdb > > > > > > Nothing comes up when I enter them. Please could someone help me with > this? > > > > > > Akash > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] what is the difference between the 2016.x and the 5.x series?
Additionally, if you care about getting the best performance on your hardware be aware that distro-packaged GROMACS versions are generally optimized for the lowest common denominator CPU architectural capabilities and will not be able to make the best use of modern CPU instructions sets. Hence, if performance matter for you, do compile from source. For more details see: http://manual.gromacs.org/documentation/2016.3/install-guide/index.html#simd-support -- Szilárd On Wed, Jul 12, 2017 at 5:51 PM, Jose Borreguerowrote: > will do, thanks for the tip. > > On Wed, Jul 12, 2017 at 11:42 AM, Mark Abraham > wrote: > > > Hi, > > > > That kind of information is in the release notes, e.g. at > > http://manual.gromacs.org/documentation/. Perhaps you want to start with > > the 2016 ones :-) > > > > Mark > > > > On Wed, Jul 12, 2017 at 5:39 PM Jose Borreguero > > wrote: > > > > > Dear Gromacs users, > > > > > > I'm a relatively new user of Gromacs and recently realized there is a > > > "2016" branch that is still being updated. What is the difference with > > the > > > 5.x branch? > > > > > > I ask because I could find RPM packages only for the 2016 version, much > > > easier to install than building from source. > > > > > > Best, > > > .Jose > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx select
I have used the same name in my coordinate file. For Glycine it is spelt as Glyci, so the word has been cut off. I know this is correct because I use the same name in VMD. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 12 July 2017 22:42 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx select Hi, What are the residue names in your coordinate file? Glyci probably doesn't fit Mark On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akashwrote: > Hi all, > > > I am trying to select all the glycine molecules with 0.5nm of my protein. > I tried both of these commands I got from the gromacs website: > > gmx select -f output.gro -select "Close to protein" resname Glyci and > within 0.5 of group "Protein"' -ofpdb > > gmx select -f output.xtc -s output.tpr (my converted input file) > -select "Close to protein" resname Glyci and within 0.5 of group > "Protein"' -ofpdb > > > Nothing comes up when I enter them. Please could someone help me with this? > > > Akash > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx select
Hi, What are the residue names in your coordinate file? Glyci probably doesn't fit Mark On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akashwrote: > Hi all, > > > I am trying to select all the glycine molecules with 0.5nm of my protein. > I tried both of these commands I got from the gromacs website: > > gmx select -f output.gro -select "Close to protein" resname Glyci and > within 0.5 of group "Protein"' -ofpdb > > gmx select -f output.xtc -s output.tpr (my converted input file) -select > "Close to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb > > > Nothing comes up when I enter them. Please could someone help me with this? > > > Akash > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx select
Hi all, I am trying to select all the glycine molecules with 0.5nm of my protein. I tried both of these commands I got from the gromacs website: gmx select -f output.gro -select "Close to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb gmx select -f output.xtc -s output.tpr (my converted input file) -select "Close to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb Nothing comes up when I enter them. Please could someone help me with this? Akash -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Non-periodic COM Pulling
Hello, Is it possible to do non-periodic COM pulling using the distance function in GMX 5.14 (i.e. where the distance between the two groups is calculated ignoring pbc)? In the tutorials/online the solution seems to be to simply use a box twice the size of the largest pulling distance, but that would be very computationally expensive for me. Best, Dan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Help on MD performance, GPU has less load than CPU.
Hi, Sure. But who has data that shows that e.g. a free-energy calculation with the defaults produces lower quality observables than you get with the defaults? Mark On Wed, Jul 12, 2017 at 5:59 PM Téletchéa Stéphane < stephane.teletc...@univ-nantes.fr> wrote: > Le 11/07/2017 à 15:24, Mark Abraham a écrit : > > Guessing wildly, the cost of your simulation is probably at least double > > what the defaults would give, and for that cost, I'd want to know why. > > Estimated colleague, > > Since this is a wild guess, I'd think to add some guesses myself. I > remember "some time" back having used a lower tolerance on Ewald for > amber simulations (around amber 4/5/6 ...) and it was more common at > this time I presume. This may also be linked to the fact that amber has > a short cut-off at 8 angstrom for electrostatics ... > Someone apparently "ill" at the time already found this stane in 2009: > > > http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/vTjpMdwU/gromacs-preformance-versus-amber > > Out of my memroy, I remembered using 10-6 for Ewald tolerance in AMBER, > and this is mentioned here: > > http://ambermd.org/Questions/ewald.html > > ... apparently linked to DNA simulation as found in JACS 117,4193 (1995) > > In short, this value may come in back and forth for "historical" reasons > (and misuse, of course). > > Others may have additional comments :-) > > Best, > > Stéphane > > > -- > Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein > Design In Silico > UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 > Nantes cedex 03, France > Tél : +33 251 125 636 / Fax : +33 251 125 632 > http://www.ufip.univ-nantes.fr/ - http://www.steletch.org > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
Hi, You need to have a file that contains the frame you want to start from, and give that to gmx grompp -t Mark On Wed, Jul 12, 2017 at 5:54 PM CLARK NICOLAS Joanwrote: > Dear gmx users, > > > I am trying to extend a finished simulation from a frame which is not the > last one in my trajectory. I have tried convert-tpr but I think it's only > modifying the number of steps because the resulting tpr file starts the > simulation from the first or the last frame depending on whether or not I > supply the cpt file to mdrun. > > > Is there any way to do what I am trying or is using grompp every time my > only choice? > > > Thanks, > > Joan > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Help on MD performance, GPU has less load than CPU.
Le 11/07/2017 à 15:24, Mark Abraham a écrit : Guessing wildly, the cost of your simulation is probably at least double what the defaults would give, and for that cost, I'd want to know why. Estimated colleague, Since this is a wild guess, I'd think to add some guesses myself. I remember "some time" back having used a lower tolerance on Ewald for amber simulations (around amber 4/5/6 ...) and it was more common at this time I presume. This may also be linked to the fact that amber has a short cut-off at 8 angstrom for electrostatics ... Someone apparently "ill" at the time already found this stane in 2009: http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/vTjpMdwU/gromacs-preformance-versus-amber Out of my memroy, I remembered using 10-6 for Ewald tolerance in AMBER, and this is mentioned here: http://ambermd.org/Questions/ewald.html ... apparently linked to DNA simulation as found in JACS 117,4193 (1995) In short, this value may come in back and forth for "historical" reasons (and misuse, of course). Others may have additional comments :-) Best, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Dear gmx users, I am trying to extend a finished simulation from a frame which is not the last one in my trajectory. I have tried convert-tpr but I think it's only modifying the number of steps because the resulting tpr file starts the simulation from the first or the last frame depending on whether or not I supply the cpt file to mdrun. Is there any way to do what I am trying or is using grompp every time my only choice? Thanks, Joan The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] what is the difference between the 2016.x and the 5.x series?
will do, thanks for the tip. On Wed, Jul 12, 2017 at 11:42 AM, Mark Abrahamwrote: > Hi, > > That kind of information is in the release notes, e.g. at > http://manual.gromacs.org/documentation/. Perhaps you want to start with > the 2016 ones :-) > > Mark > > On Wed, Jul 12, 2017 at 5:39 PM Jose Borreguero > wrote: > > > Dear Gromacs users, > > > > I'm a relatively new user of Gromacs and recently realized there is a > > "2016" branch that is still being updated. What is the difference with > the > > 5.x branch? > > > > I ask because I could find RPM packages only for the 2016 version, much > > easier to install than building from source. > > > > Best, > > .Jose > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF
Dear Vidya.R Its very difficult to answer this question.It depends on your system .If you run more time of your system, RDF will be more smooth Saikat Pal IIT GUWAHATI On Wednesday 12 July 2017, 10:02:30 AM IST, Vidya Rwrote: Hi, I want to calculate RDF of my organic molecule with a solvent. What should be the duration of my simulation? Is 100 ps enough? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] what is the difference between the 2016.x and the 5.x series?
Hi, That kind of information is in the release notes, e.g. at http://manual.gromacs.org/documentation/. Perhaps you want to start with the 2016 ones :-) Mark On Wed, Jul 12, 2017 at 5:39 PM Jose Borreguerowrote: > Dear Gromacs users, > > I'm a relatively new user of Gromacs and recently realized there is a > "2016" branch that is still being updated. What is the difference with the > 5.x branch? > > I ask because I could find RPM packages only for the 2016 version, much > easier to install than building from source. > > Best, > .Jose > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] what is the difference between the 2016.x and the 5.x series?
Dear Gromacs users, I'm a relatively new user of Gromacs and recently realized there is a "2016" branch that is still being updated. What is the difference with the 5.x branch? I ask because I could find RPM packages only for the 2016 version, much easier to install than building from source. Best, .Jose -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LINCS warning during constrained md
Hi, I would avoid using the combination of position restraints and constrained bonds with an input structure that is not necessarily consistent with the constraints. That's a recipe for large forces. I wouldn't use position restraints in such a process unless I had some reason to believe that my starting structure was special *and* saw a large deformation if I didn't use the restraints. If I saw the deformation, I would wonder why I thought it was special. If you're trying to relax a thing, let it relax. :-) If something strange happens, consider that when it has happened. Obviously that means you want to look at what happens when you did your equilibration, but you were going to do that anyway. Right? ;-) Mark On Wed, Jul 12, 2017 at 5:17 PM edesantiswrote: > hi, > > I've seen with vmd the gro file generated after the transformation, and > after the 2 steps of minimization, > it seems that they have no problem, > while if I see the step_n.pdb file generated before the crash, there are > some atoms far away from the rest of the protein, while this is not > happening if I comment the restrains part > > > do you understand why?? > > thank you again, > Emiliano > > > > On 2017-07-12 16:29, Mark Abraham wrote: > > Hi, > > > > Those are all good things, but have you actually got out a molecular > > viewer > > and looked at the input and output of your resolution conversion? > > > > Mark > > > > On Wed, Jul 12, 2017 at 4:25 PM edesantis > > wrote: > > > >> Hi, > >> thanks for the prompt answer, > >> > >> > >> I've found the same problem even if I try to convert the coarse > >> grained > >> pdb obtained from martinize.py, so in that case it should be not a > >> problem to have the conversion, for this reason I though it is a > >> methodological problem... > >> > >> I've seen the blowing-up issues , but I think: > >> - the timestep is enough small (0.0002) > >> -the system should be enough minimized via the previous steps (in fact > >> the sd converged to the machine precision in both cases, actually the > >> potential energy is ~10^5, but I don't know how to reduce it, I tried > >> a > >> cg after the sd, but the proble is still there) > >> -there in not any pressure coupling > >> -I've tried a different temperature coupling (berensden, nose-hoover) > >> and it doesn't work > >> - the md stops at the first step, so there is not any .edr file > >> produced > >> to be looked at > >> > >> > >> > >> I don't know what else to do... > >> > >> maybe, do you know another conversion protocol to use?? > >> > >> > >> thank you again > >> Emiliano > >> > >> On 2017-07-12 15:11, Mark Abraham wrote: > >> > Hi, > >> > > >> > Sounds like you might be > >> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because > the > >> > conversion doesn't work for your configuration. You should start by > >> > doing a > >> > visual check of the configuration for sanity, then follow the advice > in > >> > that link. > >> > > >> > Mark > >> > > >> > On Wed, Jul 12, 2017 at 3:04 PM edesantis > >> > wrote: > >> > > >> >> dear all, > >> >> > >> >> I am facing a problem with the conversion from Martini CG > >> >> representation > >> >> to All-atomistic one. > >> >> > >> >> I am using the initram.sh wrapper around the backward.py. > >> >> > >> >> There is a LINCS warning problem when the energy relaxation is > >> >> performed > >> >> using position restrained md > >> >> (I've also tried to run grompp and mdrun commands directly from the > >> >> terminal and the error persists, so it is not a wrapper problem). > >> >> > >> >> this is the .mdp file generated by the script: > >> >> > >> >> "define = -DPOSRES > >> >> integrator = md > >> >> nsteps = 500 > >> >> dt = 0.0002 > >> >> pbc = xyz > >> >> > >> >> rcoulomb = 0.9 > >> >> rlist= 0.9 > >> >> rvdw = 0.9 > >> >> > >> >> tcoupl = v-rescale > >> >> ref_t= 200 > >> >> tau_t= 0.1 > >> >> tc_grps = System > >> >> > >> >> gen_vel = yes > >> >> gen_temp = 300 > >> >> > >> >> constraints = all-bonds " > >> >> > >> >> > >> >> this is the error I found in the .log file: > >> >> > >> >> "Fatal error: > >> >> Too many LINCS warnings (1034) > >> >> If you know what you are doing you can adjust the lincs warning > >> >> threshold in your mdp file > >> >> or set the environment variable GMX_MAXCONSTRWARN to -1, > >> >> but normally it is better to fix the problem " > >> >> > >> >> I tired to comment the constrains part and all is working, but since > >> >> the > >> >> structure should not be altered too much, I think the constraints are > >> >> required (if I constrain only the h-bonds, it is also working). > >> >> > >> >> I've also added to the .mdp
Re: [gmx-users] LINCS warning during constrained md
hi, I've seen with vmd the gro file generated after the transformation, and after the 2 steps of minimization, it seems that they have no problem, while if I see the step_n.pdb file generated before the crash, there are some atoms far away from the rest of the protein, while this is not happening if I comment the restrains part do you understand why?? thank you again, Emiliano On 2017-07-12 16:29, Mark Abraham wrote: Hi, Those are all good things, but have you actually got out a molecular viewer and looked at the input and output of your resolution conversion? Mark On Wed, Jul 12, 2017 at 4:25 PM edesantiswrote: Hi, thanks for the prompt answer, I've found the same problem even if I try to convert the coarse grained pdb obtained from martinize.py, so in that case it should be not a problem to have the conversion, for this reason I though it is a methodological problem... I've seen the blowing-up issues , but I think: - the timestep is enough small (0.0002) -the system should be enough minimized via the previous steps (in fact the sd converged to the machine precision in both cases, actually the potential energy is ~10^5, but I don't know how to reduce it, I tried a cg after the sd, but the proble is still there) -there in not any pressure coupling -I've tried a different temperature coupling (berensden, nose-hoover) and it doesn't work - the md stops at the first step, so there is not any .edr file produced to be looked at I don't know what else to do... maybe, do you know another conversion protocol to use?? thank you again Emiliano On 2017-07-12 15:11, Mark Abraham wrote: > Hi, > > Sounds like you might be > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the > conversion doesn't work for your configuration. You should start by > doing a > visual check of the configuration for sanity, then follow the advice in > that link. > > Mark > > On Wed, Jul 12, 2017 at 3:04 PM edesantis > wrote: > >> dear all, >> >> I am facing a problem with the conversion from Martini CG >> representation >> to All-atomistic one. >> >> I am using the initram.sh wrapper around the backward.py. >> >> There is a LINCS warning problem when the energy relaxation is >> performed >> using position restrained md >> (I've also tried to run grompp and mdrun commands directly from the >> terminal and the error persists, so it is not a wrapper problem). >> >> this is the .mdp file generated by the script: >> >> "define = -DPOSRES >> integrator = md >> nsteps = 500 >> dt = 0.0002 >> pbc = xyz >> >> rcoulomb = 0.9 >> rlist= 0.9 >> rvdw = 0.9 >> >> tcoupl = v-rescale >> ref_t= 200 >> tau_t= 0.1 >> tc_grps = System >> >> gen_vel = yes >> gen_temp = 300 >> >> constraints = all-bonds " >> >> >> this is the error I found in the .log file: >> >> "Fatal error: >> Too many LINCS warnings (1034) >> If you know what you are doing you can adjust the lincs warning >> threshold in your mdp file >> or set the environment variable GMX_MAXCONSTRWARN to -1, >> but normally it is better to fix the problem " >> >> I tired to comment the constrains part and all is working, but since >> the >> structure should not be altered too much, I think the constraints are >> required (if I constrain only the h-bonds, it is also working). >> >> I've also added to the .mdp file the lines: >> " lincs-order = 4 (or 2 or 8) >> lincs-iter = 1 (or 2 or 10) >> " >> but it is still not working... >> >> >> any of you have suggestions to solve the problem?? >> how is it possible to change the environment variable? >> >> >> thanks in advance for your help >> Emiliano >> >> -- >> Emiliano De Santis >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> -- Emiliano De Santis -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Emiliano De Santis -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists *
[gmx-users] Solvent Accessible Surface Area (SASA): Separate Hydrophobic and Hydrophilic components
Hi, I want to measure the Hydrophobic and Hydrophilic components of the Solvent Accessible Surface Area. In the Tool Changes for 5.0 I found these command: gmx sasa -s md.tpr -f md_traj.trr -surface 'group "A"' -output '"Hydrophobic" group "A" and charge {-0.2 to 0.2}; "Hydrophilic" group "B" and not charge {-0.2 to 0.2}; "Total" group "B"' And I tried changing "A" and "B" for "protein", but it is not working for me. Could you show me an specific example that worked for you? Thanks very much, Núria -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LINCS warning during constrained md
Hi, Those are all good things, but have you actually got out a molecular viewer and looked at the input and output of your resolution conversion? Mark On Wed, Jul 12, 2017 at 4:25 PM edesantiswrote: > Hi, > thanks for the prompt answer, > > > I've found the same problem even if I try to convert the coarse grained > pdb obtained from martinize.py, so in that case it should be not a > problem to have the conversion, for this reason I though it is a > methodological problem... > > I've seen the blowing-up issues , but I think: > - the timestep is enough small (0.0002) > -the system should be enough minimized via the previous steps (in fact > the sd converged to the machine precision in both cases, actually the > potential energy is ~10^5, but I don't know how to reduce it, I tried a > cg after the sd, but the proble is still there) > -there in not any pressure coupling > -I've tried a different temperature coupling (berensden, nose-hoover) > and it doesn't work > - the md stops at the first step, so there is not any .edr file produced > to be looked at > > > > I don't know what else to do... > > maybe, do you know another conversion protocol to use?? > > > thank you again > Emiliano > > On 2017-07-12 15:11, Mark Abraham wrote: > > Hi, > > > > Sounds like you might be > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the > > conversion doesn't work for your configuration. You should start by > > doing a > > visual check of the configuration for sanity, then follow the advice in > > that link. > > > > Mark > > > > On Wed, Jul 12, 2017 at 3:04 PM edesantis > > wrote: > > > >> dear all, > >> > >> I am facing a problem with the conversion from Martini CG > >> representation > >> to All-atomistic one. > >> > >> I am using the initram.sh wrapper around the backward.py. > >> > >> There is a LINCS warning problem when the energy relaxation is > >> performed > >> using position restrained md > >> (I've also tried to run grompp and mdrun commands directly from the > >> terminal and the error persists, so it is not a wrapper problem). > >> > >> this is the .mdp file generated by the script: > >> > >> "define = -DPOSRES > >> integrator = md > >> nsteps = 500 > >> dt = 0.0002 > >> pbc = xyz > >> > >> rcoulomb = 0.9 > >> rlist= 0.9 > >> rvdw = 0.9 > >> > >> tcoupl = v-rescale > >> ref_t= 200 > >> tau_t= 0.1 > >> tc_grps = System > >> > >> gen_vel = yes > >> gen_temp = 300 > >> > >> constraints = all-bonds " > >> > >> > >> this is the error I found in the .log file: > >> > >> "Fatal error: > >> Too many LINCS warnings (1034) > >> If you know what you are doing you can adjust the lincs warning > >> threshold in your mdp file > >> or set the environment variable GMX_MAXCONSTRWARN to -1, > >> but normally it is better to fix the problem " > >> > >> I tired to comment the constrains part and all is working, but since > >> the > >> structure should not be altered too much, I think the constraints are > >> required (if I constrain only the h-bonds, it is also working). > >> > >> I've also added to the .mdp file the lines: > >> " lincs-order = 4 (or 2 or 8) > >> lincs-iter = 1 (or 2 or 10) > >> " > >> but it is still not working... > >> > >> > >> any of you have suggestions to solve the problem?? > >> how is it possible to change the environment variable? > >> > >> > >> thanks in advance for your help > >> Emiliano > >> > >> -- > >> Emiliano De Santis > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > -- > Emiliano De Santis > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LINCS warning during constrained md
Hi, thanks for the prompt answer, I've found the same problem even if I try to convert the coarse grained pdb obtained from martinize.py, so in that case it should be not a problem to have the conversion, for this reason I though it is a methodological problem... I've seen the blowing-up issues , but I think: - the timestep is enough small (0.0002) -the system should be enough minimized via the previous steps (in fact the sd converged to the machine precision in both cases, actually the potential energy is ~10^5, but I don't know how to reduce it, I tried a cg after the sd, but the proble is still there) -there in not any pressure coupling -I've tried a different temperature coupling (berensden, nose-hoover) and it doesn't work - the md stops at the first step, so there is not any .edr file produced to be looked at I don't know what else to do... maybe, do you know another conversion protocol to use?? thank you again Emiliano On 2017-07-12 15:11, Mark Abraham wrote: Hi, Sounds like you might be http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the conversion doesn't work for your configuration. You should start by doing a visual check of the configuration for sanity, then follow the advice in that link. Mark On Wed, Jul 12, 2017 at 3:04 PM edesantiswrote: dear all, I am facing a problem with the conversion from Martini CG representation to All-atomistic one. I am using the initram.sh wrapper around the backward.py. There is a LINCS warning problem when the energy relaxation is performed using position restrained md (I've also tried to run grompp and mdrun commands directly from the terminal and the error persists, so it is not a wrapper problem). this is the .mdp file generated by the script: "define = -DPOSRES integrator = md nsteps = 500 dt = 0.0002 pbc = xyz rcoulomb = 0.9 rlist= 0.9 rvdw = 0.9 tcoupl = v-rescale ref_t= 200 tau_t= 0.1 tc_grps = System gen_vel = yes gen_temp = 300 constraints = all-bonds " this is the error I found in the .log file: "Fatal error: Too many LINCS warnings (1034) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem " I tired to comment the constrains part and all is working, but since the structure should not be altered too much, I think the constraints are required (if I constrain only the h-bonds, it is also working). I've also added to the .mdp file the lines: " lincs-order = 4 (or 2 or 8) lincs-iter = 1 (or 2 or 10) " but it is still not working... any of you have suggestions to solve the problem?? how is it possible to change the environment variable? thanks in advance for your help Emiliano -- Emiliano De Santis -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Emiliano De Santis -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LINCS warning during constrained md
Hi, Sounds like you might be http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the conversion doesn't work for your configuration. You should start by doing a visual check of the configuration for sanity, then follow the advice in that link. Mark On Wed, Jul 12, 2017 at 3:04 PM edesantiswrote: > dear all, > > I am facing a problem with the conversion from Martini CG representation > to All-atomistic one. > > I am using the initram.sh wrapper around the backward.py. > > There is a LINCS warning problem when the energy relaxation is performed > using position restrained md > (I've also tried to run grompp and mdrun commands directly from the > terminal and the error persists, so it is not a wrapper problem). > > this is the .mdp file generated by the script: > > "define = -DPOSRES > integrator = md > nsteps = 500 > dt = 0.0002 > pbc = xyz > > rcoulomb = 0.9 > rlist= 0.9 > rvdw = 0.9 > > tcoupl = v-rescale > ref_t= 200 > tau_t= 0.1 > tc_grps = System > > gen_vel = yes > gen_temp = 300 > > constraints = all-bonds " > > > this is the error I found in the .log file: > > "Fatal error: > Too many LINCS warnings (1034) > If you know what you are doing you can adjust the lincs warning > threshold in your mdp file > or set the environment variable GMX_MAXCONSTRWARN to -1, > but normally it is better to fix the problem " > > I tired to comment the constrains part and all is working, but since the > structure should not be altered too much, I think the constraints are > required (if I constrain only the h-bonds, it is also working). > > I've also added to the .mdp file the lines: > " lincs-order = 4 (or 2 or 8) > lincs-iter = 1 (or 2 or 10) > " > but it is still not working... > > > any of you have suggestions to solve the problem?? > how is it possible to change the environment variable? > > > thanks in advance for your help > Emiliano > > -- > Emiliano De Santis > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Walls and PME for long range electrostatics
Dear all, I am simulating a Au(111) slab with explicit electrons inside (included as a "free electron gas"). The gold atoms are frozen, the electrons are free but confined inside the slab by a more repulsive pair interaction with the Au-surface atoms. This works fine and simulations are stable. I am using a xy-periodicity. For this I introduced walls on both sides of the box. My wall-atoms dont interact with any of my atoms. For a couple weeks now, I have been trying to reproduce image charge effects with this model, freezing a test charge (no LJ-interaction, only a charge of +1e assigned to it) at a certain distance from the Au surface. In the documentation it is stated that z_box should be 3 times as big as the system when using walls with a slab geometry. I did this. But the forces I calculate on the test charge neither match for the far field, nor for the near field. Do you have any suggestions on how the walls and therefore PME might bring artifacts in? I am running out of ideas on how to fix this problem. Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] LINCS warning during constrained md
dear all, I am facing a problem with the conversion from Martini CG representation to All-atomistic one. I am using the initram.sh wrapper around the backward.py. There is a LINCS warning problem when the energy relaxation is performed using position restrained md (I've also tried to run grompp and mdrun commands directly from the terminal and the error persists, so it is not a wrapper problem). this is the .mdp file generated by the script: "define = -DPOSRES integrator = md nsteps = 500 dt = 0.0002 pbc = xyz rcoulomb = 0.9 rlist= 0.9 rvdw = 0.9 tcoupl = v-rescale ref_t= 200 tau_t= 0.1 tc_grps = System gen_vel = yes gen_temp = 300 constraints = all-bonds " this is the error I found in the .log file: "Fatal error: Too many LINCS warnings (1034) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem " I tired to comment the constrains part and all is working, but since the structure should not be altered too much, I think the constraints are required (if I constrain only the h-bonds, it is also working). I've also added to the .mdp file the lines: " lincs-order = 4 (or 2 or 8) lincs-iter = 1 (or 2 or 10) " but it is still not working... any of you have suggestions to solve the problem?? how is it possible to change the environment variable? thanks in advance for your help Emiliano -- Emiliano De Santis -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ACETONITRILE with CHARM ff
> > Message: 3 > Date: Tue, 11 Jul 2017 12:57:05 -0400 > From: Justin Lemkul> > Moreover, I observed that this time I got lower values for P during the NPT > > equilibration, but still is too far from 1 bar. I really don't understand > > why for the NVT simulation I get a T around 298, but as soon as I turn on > > the pcoupl, the T rises to 300-301 K and the P gets average values of 7 > > and 4 bar (vs 8 and 14 for the previous simulations). Then at the end of > > the 1-ns MD the temperature remains around 301 and the P is -1 and 2.7 > > bar. Considering the parameters I am using, is there anything I can change > > to make the P coupling better? I am running a 3 nm box with 308 molecules. > > This is the full mdp file: > > > > http://www.gromacs.org/Documentation/Terminology/Pressure > > Your box is very small and will be subject to large fluctuations. Dear Justin, I increased the size of the simulation box to 4 nm. Indeed, the values of pressure improved (averages around -1 bar or 1.5, 2 bar, or so). However, the T keeps being overestimated (302 K). During NVT I got the right value, so I decided to run the 200 ns NPT equilibration with Berendsen barostat instead of P-R. I got the right T value, around 298.3 and a pressure of 1.5 more or less. Then I launched a continuation test with 200 ps MD with P-R (I couldn't use the -e option because it gives me the error Could not find energy term named 'Box-Vel-XX', moreover, I didn't use P-R before so I guess I shouldn't expect stored values for it?. But I am using -t ). Despite I got low pressure averages around 0.5 bar, the temperature raised again to 301-302. This happens very early in the simulation, which seems to indicate that for sd integrator/thermostat and P-R barostat there is something going on. I am getting practically the same density in between simulation, so I guess I can say tha t in term of P, the system has been equilibrated. However, what can I do to get the right T for this system? If I was able to get the right T with Berendsen barostat, I don't understand what's wrong when I change to P-R. Thank you in advance, Sonia Aguilera PhD student ENSCM > > -Justin > > > ; Run control > > integrator = sd ; Langevin dynamics > > tinit= 0 > > dt = 0.0005 > > nsteps = 200 ; 1 ns > > nstcomm = 100 > > ;energygrps = non-Water > > ; Neighborsearching and short-range nonbonded interactions > > cutoff-scheme= verlet > > nstlist = 20 > > ns_type = grid > > pbc = xyz > > rlist= 1.2 > > ; Electrostatics > > coulombtype = PME > > rcoulomb = 1.2 > > ; van der Waals > > vdwtype = cutoff > > vdw-modifier = force-switch > > rvdw-switch = 1.0 > > rvdw = 1.2 > > ; Apply long range dispersion corrections for Energy and Pressure > > DispCorr = no > > ; Spacing for the PME/PPPM FFT grid > > fourierspacing = 0.12 > > ; EWALD/PME/PPPM parameters > > pme_order= 6 > > ewald_rtol = 1e-06 > > epsilon_surface = 0 > > ; Temperature coupling > > ; tcoupl is implicitly handled by the sd integrator > > tc_grps = system > > tau_t= 1.0 > > ref_t= 298.15 > > ; Pressure coupling is on for NPT > > Pcoupl = Parrinello-Rahman > > tau_p= 1.0 > > compressibility = 4.5e-05 > > ref_p= 1.0 > > ; Do not generate velocities > > gen_vel = no > > ; options for bonds > > constraints = none ; we only have C-H bonds here > > ; Type of constraint algorithm > > constraint-algorithm = lincs > > ; Constrain the starting configuration > > ; since we are continuing from NPT > > continuation = yes > > ; Highest order in the expansion of the constraint coupling matrix > > lincs-order = 12 > > > > > > Thank you very much, > > > > Sonia Aguilera > > PhD student > > ENSCM > >> ; Run control > >> integrator = sd ; Langevin dynamics > >> tinit= 0 > >> dt = 0.0005 > >> nsteps = 4000 ; 20 ns > >> nstcomm = 100 > >> ; Neighborsearching and short-range nonbonded interactions > >> cutoff-scheme= verlet > >> nstlist = 20 > >> ns_type = grid > >> pbc = xyz > >> rlist= 1.2 > >> ; Electrostatics > >> coulombtype = PME > >> rcoulomb = 1.2 > >> ; van der Waals > >> vdwtype = cutoff > >> vdw-modifier = potential-switch > >> rvdw-switch = 1.0 > >> rvdw = 1.2 > >> ;
Re: [gmx-users] output pdb reformatted
Hi, Please stop doing that. You're risking wasting your own time as well. ;-) Mark On Tue, Jul 11, 2017 at 11:52 PM Alexwrote: > You are absolutely right once again. I've been glancing over that topology, > looking right at what the problem was, and not seeing it. The residue name > column was empty, all atom types went to crap, but because I always grompp > with -maxwarn 10 (for completely unrelated warnings in completely different > simulations) everything seemed okay. > > Thanks! > > Alex > > On Tue, Jul 11, 2017 at 2:40 PM, Justin Lemkul wrote: > > > > > > > On 7/11/17 4:01 PM, Alex wrote: > > > >> Hi all, > >> > >> I have a tiny acetonitrile molecule here. The input pdb prior to EM is > >> this: > >> > >> TITLE Gromacs Runs On Most of All Computer Systems > >> REMARKTHIS IS A SIMULATION BOX > >> CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 > >> MODEL1 > >> ATOM 1 CT ACT 1 14.870 14.744 14.594 1.00 0.00 > >>C > >> ATOM 2 HC ACT 1 15.390 13.760 14.594 1.00 0.00 > >>H > >> ATOM 3 HC ACT 1 13.769 14.581 14.594 1.00 0.00 > >>H > >> ATOM 4 HC ACT 1 15.162 15.317 13.685 1.00 0.00 > >>H > >> ATOM 5 CZ ACT 1 15.253 15.501 15.794 1.00 0.00 > >>C > >> ATOM 6 NZ ACT 1 15.555 16.097 16.740 1.00 0.00 > >>N > >> TER > >> ENDMDL > >> > >> The output, however, is this: > >> > >> TITLE Great Red Owns Many ACres of Sand > >> REMARKTHIS IS A SIMULATION BOX > >> CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 1 > >> MODEL1 > >> ATOM 1 1CT 1 15.013 15.013 14.819 1.00 0.00 > >>C > >> ATOM 2 1HC 1 14.952 13.831 14.385 1.00 0.00 > >>H > >> ATOM 3 1HC 1 13.827 14.934 14.400 1.00 0.00 > >>H > >> ATOM 4 1HC 1 15.140 15.157 13.573 1.00 0.00 > >>H > >> ATOM 5 2CZ 1 15.821 15.819 16.308 1.00 0.00 > >>C > >> ATOM 6 2NZ 1 16.401 16.397 17.446 1.00 0.00 > >>N > >> TER > >> ENDMDL > >> > >> Why? I don't think I've seen this happen before, and I'd like to keep > the > >> initial format. Any suggestions? My itp is for an ACT residue, which is > >> included in the simulation topology input. > >> > >> > > mdrun gets the residue and atom names from the topology, so a dump of the > > .tpr should show something useful. It seems like something in the > topology > > has gotten broken - atom names becoming numbers, residue name becoming > the > > atom names. Bizarre. grompp should have complained loudly if there were > > mismatches between coordinates and topology. > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > > Department of Pharmaceutical Sciences > > School of Pharmacy > > Health Sciences Facility II, Room 629 > > University of Maryland, Baltimore > > 20 Penn St. > > Baltimore, MD 21201 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > http://mackerell.umaryland.edu/~jalemkul > > > > == > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/Support > > /Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] topology servers versus ff
Hello, If you want to use CHARMM for your simulations, do not use PRODRUG to construct your parameters but use ParamChem, instead. https://www.paramchem.org/ Stéphane -- Message: 2 Date: Wed, 12 Jul 2017 14:36:27 +0500 From: maria khanTo: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] topology servers versus ff. Message-ID: Content-Type: text/plain; charset="UTF-8" Dear gromacs users.. while using charmm27 can i use PRODRUG for topology building.?? when im using prodrug pdb2gmx gives me error of missing atoms but when i use charmm ff,it doesnt give me that error,so proceeding with charmm27 i made ligand topology by prodrug and used it for further simulation,when comes to adding ions step it gives me error of ""atomtypes CH3 not found"". thanks. -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. End of gromacs.org_gmx-users Digest, Vol 159, Issue 58 ** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] topology servers versus ff.
Dear gromacs users.. while using charmm27 can i use PRODRUG for topology building.?? when im using prodrug pdb2gmx gives me error of missing atoms but when i use charmm ff,it doesnt give me that error,so proceeding with charmm27 i made ligand topology by prodrug and used it for further simulation,when comes to adding ions step it gives me error of ""atomtypes CH3 not found"". thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Benchmarks v5.0
Hi there, where can I find the benchmark input files for the 2 cases reported in this paper (ion channel and ethanol-water system)? http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf Many thanks. Jony Dr Jony Castagna Sci-Tech Daresbury Keckwick Lane Daresbury Warrington WA4 4AD Tel.: +44 (0)1925 603682 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Add missing residues
http://www.charmm-gui.org/ -- Regards, Nikhil Maroli -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Add missing residues
Hello everyone, Can someone post the best tool available for building missing residues in the crystal structure? I need the complete structure (2 missing residues) for carrying out simulation studies. Thank you *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.