Re: [gmx-users] mac OS Catalina segmentation fault

Hi Paul, Thank you for your e-mail. I forgot to note that without the plumed patch, the situation remains still problematic. The vanilla versions produce the same errors (segmentation faults), even without any specific input files. Just running the command e.g. gmx(_mpi) grompp, or gmx(_mpi)

[gmx-users] gmx gangle in a for loop

Dear all, Could one kindly let me know how $i should come in gmx gangle used in a for loop to avoid syntax errors? I tested different flavors like "$i", "${i}", ..., and still the problem is here. #!/bin/bash/ for i in {1..1000} do gmx gangle -g1 vector -group1 'group $i and name C10 plus

Re: [gmx-users] defining parameters in a separate itp file

On 11/5/19 7:53 PM, Dave M wrote: Hi Justin, Will appreciate any suggestions about the error am getting with distance_restraints. Aside from using the pull code rather than this approach, I have no other suggestions. -Justin Thanks. regards, Dave On Thu, Oct 31, 2019 at 1:39 AM Dave

Re: [gmx-users] defining parameters in a separate itp file

Hi Justin, Will appreciate any suggestions about the error am getting with distance_restraints. Thanks. regards, Dave On Thu, Oct 31, 2019 at 1:39 AM Dave M wrote: > Hi Justin, > > Thanks, not sure [distance_restraints] also does not work for me. Though > pull code works (like shared by other

Re: [gmx-users] gromos force field

Hi, I'm coming late, but I may add a few words. The GROMOS force fields have been parameterized with the GROMOS software using a twin-range cutoff (0.8/1.4), but this option is no longer available in recent versions of GROMACS. However, in a recent study

Re: [gmx-users] mac OS Catalina segmentation fault

Hello, could you try running first with an unmodified version of GROMACS, so we can check if the PLUMED modifications are responsible for the crashes (unlikely for the tools, but we need to make sure)? If the vanilla versions are still crashing, can you supply us with some log files and input

[gmx-users] mac OS Catalina segmentation fault

Dear all, I am running Mac OS Catalina 10.15.1 (Xcode 11.2 11B52). I have successfully compiled several versions of Gromacs (5.1.5, 2018.8, or 2019.4) patched with plumed (v.2.4.6 for 5.1.5, or v.2.5.3 for 2018/2019 versions). The compilations are completed without any errors, employing the

Re: [gmx-users] Error in DNA.itp file

On 11/5/19 11:55 AM, Najamuddin Memon wrote: You may use Amber99sb force field for DNA-protein simulation and also put residue type.dat file in your folder. It will work The nucleic acid parameter sets packaged with these GROMACS ports are wildly outdated. I suggest finding better

Re: [gmx-users] Error in DNA.itp file

Residue type.dat file having definition of nucleotides On Tue, Nov 5, 2019, 9:55 PM Najamuddin Memon wrote: > You may use Amber99sb force field for DNA-protein simulation and also put > residue type.dat file in your folder. It will work > > > On Tue, Nov 5, 2019, 6:59 PM Paul bauer wrote: >

Re: [gmx-users] Error in DNA.itp file

You may use Amber99sb force field for DNA-protein simulation and also put residue type.dat file in your folder. It will work On Tue, Nov 5, 2019, 6:59 PM Paul bauer wrote: > Hello, > > the error states that you are missing parameters for your system. Did > you check that the forcefield

Re: [gmx-users] Slurm for GROMACS

Hi, SLURM and OpenMPI do different things. SLURM is a resource manager, from which you might request multiple compute nodes. OpenMPI is a parallelism library that allows a program to run on those nodes. GROMACS is the program, and it doesn't care which MPI library is in use, or which resource

Re: [gmx-users] Error in DNA.itp file

Hello, the error states that you are missing parameters for your system. Did you check that the forcefield contains all the special parameters you need for the conjugate molecule? Also, I would recommend to not use a prehistoric version of GROMACS for new studies, if there are no specific

[gmx-users] Slurm for GROMACS

Researchers, Is slrum required to run GROMACS on multiple computers or OpenMPI is fine? Thank you Shradheya DBT-BIF University of Rajasthan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] Error in DNA.itp file

Hi all, i am preparing system of DNA-protein complex, downloaded it from RCSB website, by using GROMACS-version 4.5.5; force field AMBER03WS with water Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type. but the problem is that when i use command for energy minimization the

Re: [gmx-users] Ruuning MD simulation on laptop

So the answer is yes, you can, but I'm not sure you should. Assuming you have a mid to high end gaming laptop - say something like a i7-8750H with a Nvidia MaxQ 1070 (i.e. a Gigabyte Aero 15x or equivalent; I'm just going with what I have), you will get decent performance (I can get circa 80

[gmx-users] (no subject)

Hi all, i am preparing system of DNA-protein complex, downloaded it from RCSB website, by using GROMACS force field AMBER03WS with water Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type. but the problem is that when i use command for energy minimization the following error

Re: [gmx-users] Regarding force field for silicon oxide

Den 2019-11-05 kl. 01:59, skrev Mijiddorj B: Dear Prof. David van der Spoel, Thank you very much for your reply and sending an amazing work. I am sorry for asking further questions. Can you give me an advice to use the parameters which were considered in the ref#44 in this work? Ref#44 uses the