[gmx-users] x2top and default dihedral type

When generating dihedrals, x2top sets the function to '1'. I recall there was a way to change that (to 3 in my case) and it worked in modified OPLS-AA. I am working with a different FF now and for the life of me cannot recall I changed that in OPLS. I could also be wrong and it just sets it to

Re: [gmx-users] membrane-protein simulation

Thanks Justin Got it, it's working. On Wed, Aug 2, 2017 at 10:02 AM, Justin Lemkul wrote: > > > On 8/2/17 5:01 AM, Amir Zeb wrote: > >> Hello gmx-user >> >> I want to simulate a membrane protein with more than one chains like A, B, >> C etc. I generated the strong_posre.itp

Re: [gmx-users] AVX related compiler error during build with P100 RHEL7

Hi, Usually this means, like it says, that the linker isn't able to do the required job. I don't know whether the stock RHEL 7.2 linker can, but I imagine that's the issue. Usually using a devtoolset e.g. https://www.softwarecollections.org/en/scls/rhscl/devtoolset-4/ is the way to get a machine

Re: [gmx-users] AVX related compiler error during build with P100 RHEL7

Any update on this one?? On Fri, Jul 14, 2017 at 1:30 PM, Guyen Gn wrote: > Any ideas on this one? Thanks! > > On Mon, Jul 3, 2017 at 9:33 PM, Guyen Gn wrote: > >> Still did not work. change xMIC to xCore and log is below (if it was >> other way around,

Re: [gmx-users] CHARMM36 for GMX

That's true, a lot of redundant stuff there and once again these are very basic forcefield facts for what biochem folks do. In my case, I have a bunch of very simple situations in crystal structures, but now I gotta use CHARMM or AMBER (lipids!) and charge assignment (half the time perfectly

[gmx-users] segmentation fault for unknown reason

Hello! I am trying to minimize a periodic MnO2 surface using UFF force fields. I have previously computed many structures using MnO2 clusters. I did not face much problem. However, when I am trying to compute the minimization using the following minim.mdp there is segmentation error as follows.

Re: [gmx-users] CHARMM36 for GMX

On 8/2/17 2:52 PM, Alex wrote: Yeah, those are indeed there for the particular molecules, thanks. I understand that this is the only way to go, it's just that my use of GMX is somewhat different in that I rarely use molecules in the normal sense, and OPLS-AA, being a LEGO for simple groups,

Re: [gmx-users] CHARMM36 for GMX

Yeah, those are indeed there for the particular molecules, thanks. I understand that this is the only way to go, it's just that my use of GMX is somewhat different in that I rarely use molecules in the normal sense, and OPLS-AA, being a LEGO for simple groups, has been very convenient with that

Re: [gmx-users] CHARMM36 for GMX

On 8/2/17 2:38 PM, Alex wrote: Huh. Most of my work has been with OPLS-AA, so I took that for granted. Where would the actual charges be, then? In the .rtp file, where residues are defined. Charges are not (and should not) necessarily be linked to atom types; they are a function of

[gmx-users] CHARMM36 for GMX

Hi all, I am not entirely sure it's a question for the Gromacs community, as this is regarding CHARMM36, but it appears that the original forcefield is fine, while I am confused by its Gromacs version. Namely this: the MacKerell website distributes a Gromacs version of CHARMM36 where

Re: [gmx-users] G_MMPBSA

Did you try the pre-compiled version from here: http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html it worked just fine with me on debian and CentOS. Offcourse you need to have APBS installed. On Thu, Jul 27, 2017 at 7:04 PM, Mark Abraham wrote: >

Re: [gmx-users] QM/MM in Gromacs-5.1.4?

Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html Also, you need to set the following variable at compile time -DGMX_QMMM_ORCA=ON -- Clinton King Graduate Student Chemistry Department Brigham Young University > Message: 3 > Date: Wed, 2 Aug 2017 15:01:29 +0200 > From: Albert

Re: [gmx-users] -multidir option in REMD (GROMACS v2016.1) -resolved

THank you Mark and Johannes, I finally resolved my problem by using your solutions and can launch my REMD simulations Best Stéphane -- Message: 1 Date: Wed, 02 Aug 2017 10:59:10 + From: Mark Abraham

Re: [gmx-users] Clayff forcefield

On 8/2/17 5:20 AM, G R wrote: I try to implement CLYFF in gromacs. I created ffbonded.itp, ffnonbonded.itp, atomtype.atp, forcefield.doc, forcefield.itp and molecule.rtp. I want to simulate Kaolinite, and I try to use pdb2gmx to create a topology. My first question is that

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

On 8/2/17 9:12 AM, Ali Ahmed wrote: Dear all, Thank you for helping me. All I get from grompp is this -- gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o topol.tpr Ignoring obsolete mdp entry 'title'

Re: [gmx-users] Error in itp file

On 8/2/17 12:35 PM, Souvik Dey wrote: Hi, I just generated an itp file from ACPYPE. However, if I try to add ions it shows the following error: Fatal error: Syntax error - File FAD.itp, line 3 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Can somebody say how do I

Re: [gmx-users] membrane-protein simulation

On 8/2/17 5:01 AM, Amir Zeb wrote: Hello gmx-user I want to simulate a membrane protein with more than one chains like A, B, C etc. I generated the strong_posre.itp file as Justing has kindly explained in his tutorial, and updated the topol.top file by inserting the same lines. I also

Re: [gmx-users] Creating Custom .rtp files

On 8/2/17 5:07 AM, Momin Ahmad wrote: I think the reason for the weird log is the "|" command that lets you write the output of another command into a file. In the case of the error i could choose the forcefield before the error occurred. The methane was called "CH4" before, i just changed

Re: [gmx-users] Error in itp file

Hi Can you tell me, how have you used ACPYPE for itp. On Aug 2, 2017 9:36 AM, "Souvik Dey" wrote: > Hi, > > I just generated an itp file from ACPYPE. However, if I try to add ions it > shows the following error: > > Fatal error: > Syntax error - File FAD.itp, line 3 >

[gmx-users] Error in itp file

Hi, I just generated an itp file from ACPYPE. However, if I try to add ions it shows the following error: Fatal error: Syntax error - File FAD.itp, line 3 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Can somebody say how do I fix this? Regards, Souvik Dey -- Souvik

[gmx-users] Fwd: meaning of -sigfac option in gmx sigeps

Hi Everyone, Can anyone help me regarding the -sigfac option in gmx sigeps? What does this -sigfac imply? The LJ potential form is U(r) = (27/4)*epsilon [ (sigma/r)^9 - (sigma/r)^6 ] -- Tamisra Pal Post Doctoral Research Fellow Technische Universität Darmstadt Institut für Festkörperphysik

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Dear all, Thank you for helping me. All I get from grompp is this -- gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o topol.tpr Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off!

[gmx-users] Dynamics only for cavity in molecule.

Hello! I want to run dynamics only for a relatively small cavity of my molecule, with all other atoms frozen. For this reason, I also don't use solvent, because it won't move anyway. I run the simulation on GPU (gromacs 5.1.2), i.e. I use the Verlet scheme, pbc = xyz. However, when I start

[gmx-users] QM/MM in Gromacs-5.1.4?

Hello, I would like to use ORCA as a QM engine for Gromacs QM/MM simulation. I am just wondering shall we add additional options to cmake when we compile Gromacs? Thanks a lot Albert -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] hole in the simulation box

thank you for your suggestion, I've tuned the gmx solvate -radius parameter until I achieved the stability of the box dimensions in the NPT ensemble, now it seem the everything is working... thanks again, regards, Emiliano On 2017-08-01 00:10, Dallas Warren wrote: There are insufficient

Re: [gmx-users] Error in the replica order in REMD (GMX v2016.1)

I solved it rather the brute force way: In the shell script which I execute to run all my simulations I defined a variable for my Multidir and filled it with all the directories (which were then in order). somewhere in the shell script: [...] MULTIDIR="" LAMBDALIST=(0 1 2 3 4 5)

Re: [gmx-users] Error in the replica order in REMD (GMX v2016.1)

Hi, The shell expansion is sorted alphabetically, rather than numerically, so the order is md_0, md_1, md_10, md_11, etc. Either make your directories like md_000, md_001, md_002, so the sortings are the same, or use a more complex wildcard like -multidir md_[0-9] md_[1-9][0-9] Mark On Wed, Aug

[gmx-users] Error in the replica order in REMD (GMX v2016.1)

Hello again Thanks to J. Hermann I can start my simulations, however few seconds after the beginning of the run I have the following error "Replicas with indices 2 < 12 have temperatures 271.9 > 254.27, please order your replicas on increasing temperature" I do not understand this error,

Re: [gmx-users] GPU job failed

Hi, My first guess is that the implementation of PLUMED doesn't support this. Does a normal non-PLUMED simulation run correctly when called in this manner? Mark On Wed, Aug 2, 2017 at 9:55 AM Albert wrote: > Hello, > > I am trying to run Gromacs with the following

Re: [gmx-users] -multidir option in REMD (GROMACS v2016.1)

Hi, On Wed, Aug 2, 2017 at 11:22 AM ABEL Stephane wrote: > Dear all, > > I would like to do a REMD of a system with 75 replicas (with 75 > directories named md_0,..., md_75) and I have two questions. > > 1) To launch the md calculation we should use the followng command :

Re: [gmx-users] -multidir option in REMD (GROMACS v2016.1)

Hi, On 02.08.2017 11:21, ABEL Stephane wrote: Dear all, I would like to do a REMD of a system with 75 replicas (with 75 directories named md_0,..., md_75) and I have two questions. 1) To launch the md calculation we should use the followng command : mpirun -np 4 mdrun_mpi -v -multidir

[gmx-users] -multidir option in REMD (GROMACS v2016.1)

Dear all, I would like to do a REMD of a system with 75 replicas (with 75 directories named md_0,..., md_75) and I have two questions. 1) To launch the md calculation we should use the followng command : mpirun -np 4 mdrun_mpi -v -multidir sim[0123] -replex XXX My question is since I have

[gmx-users] Clayff forcefield

I try to implement CLYFF in gromacs. I created ffbonded.itp, ffnonbonded.itp, atomtype.atp, forcefield.doc, forcefield.itp and molecule.rtp. I want to simulate Kaolinite, and I try to use pdb2gmx to create a topology. My first question is that should I create any other files?

Re: [gmx-users] Creating Custom .rtp files

I think the reason for the weird log is the "|" command that lets you write the output of another command into a file. In the case of the error i could choose the forcefield before the error occurred. The methane was called "CH4" before, i just changed the names for troubleshooting. This time

[gmx-users] membrane-protein simulation

Hello gmx-user I want to simulate a membrane protein with more than one chains like A, B, C etc. I generated the strong_posre.itp file as Justing has kindly explained in his tutorial, and updated the topol.top file by inserting the same lines. I also updated the minim.mdp file by inserting

[gmx-users] GPU job failed

Hello, I am trying to run Gromacs with the following command line: mpirun -np 4 gmx_mpi mdrun -v -g 7.log -s 7.tpr -x 7.xtc -c 7.gro -e 7.edr -plumed plumed.dat -ntomp 2 -gpu_id 0123 but it always failed with the following messages: Running on 1 node with total 24 cores, 48 logical cores,