[gmx-users] Can we convert a triclinic simulation box to orthogonal box in GROMACS without loosing periodicity?
Dear GROMACS users, I am trying to simulate a triclinic crystal at the center with solvent on either side in the z-direction and periodic x-y plane. The crystal box is very skewed with one of the angles from the horizontal axis is 30 degrees. I have first simulated it in the triclinic box but apparently, a box bigger in z-direction required. In doing so, I would need much larger x-y dimensions to satisfy requirements for the triclinic box ( ax>2bx, ax>2cx, by>2cy). This will increase the cost of simulation significantly. I tried using trjconv command by centering the molecule around an atom. The wrapped molecules turn out to be in the orthogonal coordinate system but the box is still triclinic. I tried removing the non-diagonal elements of the box but then crystal loses its periodicity. Is there a way I can convert this triclinic box to orthogonal without losing the periodicity of the crystal? My crystal is consist of molecules consist of 74 atoms. Please let me know if more information is needed. Thanks Lakshman -- 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] 2019.2 build warnings
Hi Szilárd, Since I don't know which directory inside /complex corresponds to which tests (at least one of the tests that failed was #42), here's a tarball of the entire /complex directory per location you specified below: https://www.dropbox.com/s/44uluopkdan2417/regression_complex_2019.2.tar.gz?dl=0 If you can help us figure this out, it will be great! Thanks, Alex On 4/29/2019 4:25 AM, Szilárd Páll wrote: Hi, I assume you used -DREGRESSIONTEST_DOWNLOAD=ON case in which the tests are downloaded and unpacked under BUILD_TREE/tests/regressiontests-release-2019-[SUFFIX]/ In that directory you find the usual regressiontests tree, from there under complex/ you'll find the tests in question. Cheers, -- Szilárd On Fri, Apr 26, 2019 at 7:00 PM Alex wrote: Hi Szilárd, I am at a conference right now, but will do my best to upload the requested data first thing on Monday. In the meantime, could you please tell me where the stuff of interest would be located within the local gromacs build directory? I mean, I could make the entire directory a tarball, but not sure it's all that necessary. I don't remember which tests failed, unfortunately... Thank you! Alex On 4/25/2019 2:54 AM, Szilárd Páll wrote: Hi Alex, On Wed, Apr 24, 2019 at 9:59 PM Alex wrote: Hi Szilárd, We are using neither Ubuntu 18.04, nor glibc 2.27, but the problem is most certainly there. OK. Can you please post the content of the directories of tests that failed? It would be useful to know the exact software configuration (reported in the log) and the details of the errors (reported in the mdrun.out). Thanks, -- Szilárd Until the issue is solved one way or another, we will be staying with 2018.1, i guess. $ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description:Ubuntu 16.04.6 LTS Release:16.04 Codename: xenial Ubuntu GLIBC 2.23-0ubuntu11 On 4/24/2019 4:57 AM, Szilárd Páll wrote: What OS are you using? There are some known issues with the Ubuntu 18.04 + glibc 2.27 which could explain the errors. -- Szilárd -- 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 might be the best way of analysis of this kind of salt bridges with Gromacs?
On 4/24/19 6:57 AM, Anna VERDINO wrote: Dear Gromacs users, I have a dimeric protein and I am interested in analysing the salt bridges between chain A and B. When I do this command: *gmx saltbr [-f [<.xtc/.trr/...>]] [-s [<.tpr>]]* after a while it is killed. I just tryed to do this command using only a frame of trajectory: *gmx saltbr [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-b ] [-e ] * but it is killed again. This is error output: *Reading file topol.tpr, VERSION 2018.2 (single precision)** /var/spool/slurmd/job1310742/**slurm_script: line 18: 22509 Killed gmx saltbr -f trj.xtc -s topol.tpr -b 0 -e 2* * slurmstepd: error: Detected 1 oom-kill event(s) in step 1310742.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.* I understand that the problem is the memory requirement. However, I don't want to calculate ALL the salt bridges present in the protein, but only those involved in interchain interactions. What might be the best way of analysis of this kind of salt bridges with Gromacs? It seems to me that with gmx saltbr I cannot specify a subgroup of residues by using -n. Can anyone help me? gmx saltbr requires a huge amount of memory as it considers any pair of charges (including mobile ions!) as being capable of participating in a salt bridge. The more judicious approach is to specifically study interatomic distances of interest, identified by prior knowledge of the structure and what you observe while watching the trajectory. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] RMSD command line doubt
On 4/28/19 9:53 PM, Neena Susan Eappen wrote: Hello gromacs users, My goal is to calculate all-atom rmsd of every structure in the trajectory(.trr) to the final structure after simulation (.gro). Q1) So, I don't understand the purpose of giving .tpr input file (which was the input structure file before production mdrun) as a structure file in the command. gmx rms -f peptide.trr -s peptide.tpr -o rmsd.xvg The .tpr contains the topology (including masses for fitting) and the reference structure to which the fit is performed. Q2) When I use final structure .gro file (after production mdrun), I get the following warning: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. This message is printed any time a coordinate file is used as reference. For a standard protein simulation with nothing fancy about it, the guessed masses are fine. If you want to be 100% sure you're getting the right masses, generate a new .tpr file from the desired coordinate file and use it for analysis. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Multiple MD simulation
On 4/23/19 2:55 AM, ISHRAT JAHAN wrote: Dear all, I have done the long 200ns MD simulation of protein in water. I have received a comment from the reviewer that for the convergence of the results I have to perform multiple simulations using different initial conformations. Can anyone tell me the criteria for taking the different initial conformations of protein and how to check the convergence of the results? Any help regarding this will be highly appreciated. What defines a different conformation depends on the system being investigated. Perhaps that means starting with a different loop conformation (if relevant) or some different state of a multi-domain protein (open vs. closed) or a different conformer of an IDP. That's up to you to determine. It is more common to start with the same conformation but different velocities. No single trajectory is necessarily believable; replicates are generally expected for any modern MD simulation study. Convergence across the ensemble simply means that the results of different simulations do not differ from one another as determined by statistical testing. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Average rmsd
On 4/25/19 8:49 AM, neelam wafa wrote: Hi! I have run 5ns simulation of protein ligand complex and got its rmsd plot using gmx_rms. How can i get average rmsd value for this simulation. Is it to be taken from xmgrace graph or there is any way to calculate it? U cant find it in log file. You can get the average of any data series (as well as other statistical analysis) with gmx analyze. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Box dimension in Umbrella Sampling
On 4/25/19 7:10 AM, SUSHMITA BASU wrote: Dear users, I am using Gromacs 2016 to do umbrella sampling of a protein-RNA complex. I am following the Lemkul's tutorial of umbrella sampling, but I couldn't get how the box dimension was determined. I understand why for a pull of 5nm, the z axis of the box is set at 12 nm, but did not get how the x and y axis of the box is determined. This question might be very basic, but I cannot figure out how to do it. Kindly help me in this. Thanks in advance. I built a standard box with editconf -d and then used the x and y box vectors and extended along z. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Question on generating hydrogens
On 4/22/19 5:39 PM, tca1 wrote: Hi all, Is it possible to use pdb2gmx to generate hydrogens for a configuration file without also creating a topology file? Based on the documentation, it seems I can only rename this file, not prevent its creation. Ideally, I'd like to prevent this, because I have many identically-structured polymer molecules and building the topology for the whole system takes a very long time, but I can use a template topology file which includes a single-chain itp file and then just tells the code how many chains are present (analogously to how solvents are handled). However, my initial input file doesn't have the hydrogens included, so I've been forced to use pdb2gmx to handle this part. I'd love to be able to decouple the steps, though. The principal function of pdb2gmx is to produce a topology. Production of a force field-compatible structure is actually somewhat of a side effect. The only way to prevent the production of a topology is to explicitly disable these functions in the code and recompile. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] question about convert Ryckaert-Bellemans dihendral to dihendral type 9
Dear all: I am trying use antichamber to generate an tpr file for a special residue. When I got the converted tpr file, I noticed that the "func" in [dihendral] is 3, that means it is a Rychaert-Bellemans dihendral. But the Amber03 forcefield use dihendral type 9(func 9). So does anyone knows how to convert Rychaert-Bellemans dihendral to dihendral type 9? I calculated the charge of this special residule by gaussian and fitted into RESP charge, then converted it to topology file in Amber forcefield. I have encountered an fatal error when I using pdb2gmx, which tells me that residues in one molecule have a different 'dihendrals' type: 9 and 3. I would appreciate any advice! Best, Minhua Zhang Institute of Plant Physiology and Ecology, SIBS, CAS mhzhan...@sibs.ac.cn -- 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 might be the best way of analysis of this kind of salt bridges with Gromacs?
Il Mer 24 Apr 2019, 12:57 Anna VERDINO ha scritto: > Dear Gromacs users, > I have a dimeric protein and I am interested in analysing the salt bridges > between chain A and B. > > When I do this command: > > *gmx saltbr [-f [<.xtc/.trr/...>]] [-s [<.tpr>]]* > > after a while it is killed. > > I just tryed to do this command using only a frame of trajectory: > > > *gmx saltbr [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-b ] [-e ] * > but it is killed again. > > This is error output: > > > *Reading file topol.tpr, VERSION 2018.2 (single precision)** > /var/spool/slurmd/job1310742/**slurm_script: line 18: 22509 Killed > gmx saltbr -f trj.xtc -s topol.tpr -b 0 -e 2* > * slurmstepd: error: Detected 1 oom-kill event(s) in step 1310742.batch > cgroup. Some of your processes may have been killed by the cgroup > out-of-memory handler.* > > I understand that the problem is the memory requirement. However, I don't > want to calculate ALL the salt bridges present in the protein, but only > those involved in interchain interactions. What might be the best way of > analysis of this kind of salt bridges with Gromacs? It seems to me that > with gmx saltbr I cannot specify a subgroup of residues by using -n. > > Can anyone help me? > > Many thanks in advance for your kind answer > > Anna > -- 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] 2019.2 build warnings
Hi, I assume you used -DREGRESSIONTEST_DOWNLOAD=ON case in which the tests are downloaded and unpacked under BUILD_TREE/tests/regressiontests-release-2019-[SUFFIX]/ In that directory you find the usual regressiontests tree, from there under complex/ you'll find the tests in question. Cheers, -- Szilárd On Fri, Apr 26, 2019 at 7:00 PM Alex wrote: > Hi Szilárd, > > I am at a conference right now, but will do my best to upload the > requested data first thing on Monday. In the meantime, could you please > tell me where the stuff of interest would be located within the local > gromacs build directory? I mean, I could make the entire directory a > tarball, but not sure it's all that necessary. I don't remember which tests > failed, unfortunately... > > Thank you! > > Alex > > On 4/25/2019 2:54 AM, Szilárd Páll wrote: > > Hi Alex, > > > > On Wed, Apr 24, 2019 at 9:59 PM Alex wrote: > > > >> Hi Szilárd, > >> > >> We are using neither Ubuntu 18.04, nor glibc 2.27, but the problem is > >> most certainly there. > > > > OK. > > > > Can you please post the content of the directories of tests that failed? > It > > would be useful to know the exact software configuration (reported in the > > log) and the details of the errors (reported in the mdrun.out). > > > > Thanks, > > -- > > Szilárd > > > > > > > >> Until the issue is solved one way or another, we > >> will be staying with 2018.1, i guess. > >> > >> $ lsb_release -a > >> > >> No LSB modules are available. > >> > >> Distributor ID: Ubuntu > >> > >> Description:Ubuntu 16.04.6 LTS > >> > >> Release:16.04 > >> > >> Codename: xenial > >> > >> Ubuntu GLIBC 2.23-0ubuntu11 > >> > >> > >> On 4/24/2019 4:57 AM, Szilárd Páll wrote: > >>> What OS are you using? There are some known issues with the Ubuntu > 18.04 > >> + > >>> glibc 2.27 which could explain the errors. > >>> -- > >>> Szilárd > >>> > >>> > >>> > >>> > >> -- > >> 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] (no subject)
ok -- 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.
