[gmx-users] regarding adaptive molecular dynamics simulation

Dear all I want to run adaptive MD simulation on GROMACS. Guide me how to proceed. Regards -- 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

Re: [gmx-users] Installing gmx_mpi

I see the typical installation now: What I understand , I hope right, is to cd to the gromacs-2018/build where I started initially the installation of normal gmx, and invoke below; (or I have to create a new build directory for a new isntallation?) ~> /gromacs-2018/build ~> cmake .. -DGMX_MPI=on

Re: [gmx-users] Installing gmx_mpi

Hi, What did you find about MPI in the "typical installation" section? Mark On Sat, Mar 17, 2018 at 12:22 AM Alex wrote: > Hi Mark, > > Thanks for your response. > > What I can find linked with mpi in the INSTALL file is below, which I is > unclear for me. > > > If you wish to run in parallel

Re: [gmx-users] Installing gmx_mpi

Hi Mark, Thanks for your response. What I can find linked with mpi in the INSTALL file is below, which I is unclear for me. If you wish to run in parallel on multiple machines across a network, you will need to have * an MPI library installed that supports the MPI 1.3 standard, and * wrapper

Re: [gmx-users] Installing gmx_mpi

Hi, The "typical installation" section covers the one thing you need to do in this case... is it unclear? Mark On Fri, Mar 16, 2018 at 11:55 PM Alex wrote: > Dear all, > > I have successfully installed gromacs 2018 in my opensuse 42.3 exactly > following the remedy provided in the INSTALL file

[gmx-users] Installing gmx_mpi

Dear all, I have successfully installed gromacs 2018 in my opensuse 42.3 exactly following the remedy provided in the INSTALL file as below: tar xfz gromacs-2018.tar.gz cd gromacs-2018 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make mak

Re: [gmx-users] Regarding minimum size

Hi, You should really take the time to understand how you set up the description of a system in the .top file. That content is serialized into the .tpr file, and present in the gmx_mtop_t type. The potential energy (and its derivatives, including the force) depend parametrically on the coordinate

Re: [gmx-users] Regarding minimum size

Hi, do_md() has a boolean about rerun that controls whether it calls the function that reads from the trajectory file Mark On Fri, Mar 16, 2018 at 11:06 PM Chhavi Yadav wrote: > Thanks a lot! > > Is there a function similar to > > read_tpx_state that reads the .gro file and in which function i

Re: [gmx-users] Regarding minimum size

Also, You said "The .tpr provides only the model physics. It won't work because the .tpr reads a configuration into the state, and then rerun reads a different one." What do you mean by model physics? If I am thinking about it correctly, then .tpr should be a file constant for all molecules or i

Re: [gmx-users] Regarding minimum size

Thanks a lot! Is there a function similar to read_tpx_state that reads the .gro file and in which function is it being called? I couldn't find it. On Fri, Mar 16, 2018 at 5:51 PM, Mark Abraham wrote: > Hi, > > On Fri, Mar 16, 2018 at 10:43 PM Chhavi Yadav wrote: > > > Hello, > > > > So here

Re: [gmx-users] Regarding minimum size

Hi, On Fri, Mar 16, 2018 at 10:43 PM Chhavi Yadav wrote: > Hello, > > So here is what I want to do. Kindly help. > > I generate .gro and .top from .pdb file using pdb2gmx command. Then using > .gro and .top I generate .tpr with the grompp command. Then using .tpr and > .gro files I generate the

Re: [gmx-users] Regarding minimum size

Hello, So here is what I want to do. Kindly help. I generate .gro and .top from .pdb file using pdb2gmx command. Then using .gro and .top I generate .tpr with the grompp command. Then using .tpr and .gro files I generate the .edr file using mdrun -rerun. Issue 1: When I change the coordinates of

Re: [gmx-users] Regarding minimum size

Hi, Change the contents of the file on disk... Again, whatever you are trying to do should be approached in a totally different way. Mark On Fri, Mar 16, 2018 at 9:43 PM Chhavi Yadav wrote: > I basically want to change the atom coordinates in the variable where the > gro file contents are read

Re: [gmx-users] nve energy conservation

Hi, On Fri, Mar 16, 2018 at 7:42 PM Jo wrote: > Thank you for your reply! > > I am attempting to conserve energy in an NVE run of 1000 SPCE water - I > have tried a number of different verlet-buffer-tolerances (0.001 to 5e-5), > sometimes the run output file suggests a specific verlet buffer-tol

Re: [gmx-users] Regarding minimum size

I basically want to change the atom coordinates in the variable where the gro file contents are read and stored. So I want to change the contents of that variable. On Fri, Mar 16, 2018 at 4:39 PM, Chhavi Yadav wrote: > Hello, > > I wanted to know which function calls another function(which one i

Re: [gmx-users] Regarding minimum size

Hello, I wanted to know which function calls another function(which one is this too) that prints the following: starting md rerun 'LYSOZYME', reading coordinates from input trajectory '1aki/1AKI.gro' Reading frames from gro file 'LYSOZYME;', 1960 atoms. Reading frame 0 time0.000 Kind

Re: [gmx-users] nve energy conservation

Thank you for your reply! I am attempting to conserve energy in an NVE run of 1000 SPCE water - I have tried a number of different verlet-buffer-tolerances (0.001 to 5e-5), sometimes the run output file suggests a specific verlet buffer-tolerance. However I am still experiencing ~600 kJ/mol shift

[gmx-users] mdp options for Amber99sb-ildn

Dear Gromacs Users I am trying to run a molecular dynamics simulation of DNA by amber99sb-ildn forcefield. The topology has been generated successfully, the solvent and ions has been added. I would like to know how to determine the mdp file options in minimization and equilibration step for the A

Re: [gmx-users] QM/MM optimization in gromacs/gaussian (nikol...@spbau.ru)

Hi, Is the potential energy still going down, despite the rupture of the QM region? Input is same for EM and MD, and the fact that you can perform QM/MM dynamics looks promising. Are you using constraints ? What happens if you do 100 steps of CG, using jus MM,but all other parameters the same?

[gmx-users] Simulation of D-Alanine (prasun kumar)

Hi I added the same problems few days ago.There is no hdb entries for D-AA, so GROMACS can not generate the missing Hs. So I would suggest you to use CHARMM-GUI, instead and use a fake *.itp with the L-ALA (ALA) renamed to DALA. Good luck Stéphane -- Hi Group:

Re: [gmx-users] Reg. mdrun error: not all ion group molecules consist of 3 atoms

Hi, > On 16. Mar 2018, at 02:39, 가디 장데부 고라크스나트 wrote: > > Hello,I am performing computational Electrophysiology gromacs tutorial. I > successfully pass the grompp for the compEL but failed with a Fatal error at > mdrun step, not all ion group molecules consist of 3 atoms.my command for > gro

[gmx-users] Simulation of D-Alanine

Hi Group: I am trying to simulate a peptide containing D-Alanine (DAL). For this purpose, I am using Charmm36m Force Field. While running the command 'pdb2gmx -f input.pdb -ignh -ff charmm36-july17', I got an error saying 'DAL is not defined' (something similar to this). I understand that the resi