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

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

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

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

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

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

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

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

Re: [gmx-users] Regarding minimum size

Hi, On Tue, Mar 13, 2018 at 4:11 PM Chhavi Yadav wrote: > Hi, > > why is calling mdrunner twice a problem? > Because nobody wrote the code with that in mind. There's a lot of things that are built around the assumption that mdrun will start, and then stop, and nothing happens

Re: [gmx-users] Regarding minimum size

Hi, why is calling mdrunner twice a problem? I get the correct value when mdrunner runs the first time. Why do I get the error only during the second time considering I am not anyway doing any settings during both the times? Thanks, Chhavi On Mon, Mar 12, 2018 at 6:24 PM, Mark Abraham

Re: [gmx-users] Regarding minimum size

Hi, That's not a valid way to use these components. Whatever you're trying to do shouldn't be attempted by trying to call mdrunner.mainFunction() twice. Mark On Mon, Mar 12, 2018 at 9:54 PM Chhavi Yadav wrote: > I wrote this code and was running the debugger: > > > int

Re: [gmx-users] Regarding minimum size

On 3/12/18 4:52 PM, Chhavi Yadav wrote: I wrote this code and was running the debugger: int main(int argc, char *argv[]) { int rc; MD mdrunner; rc = mdrunner.mainFunction(argc, argv); printf("Potential Energy from integrator: %.6f\n", mdrunner.epot); mdrunner.epot

Re: [gmx-users] Regarding minimum size

I wrote this code and was running the debugger: int main(int argc, char *argv[]) { int rc; MD mdrunner; rc = mdrunner.mainFunction(argc, argv); printf("Potential Energy from integrator: %.6f\n", mdrunner.epot); mdrunner.epot = 0; t_state *t =

Re: [gmx-users] Regarding minimum size

On 3/12/18 2:05 PM, Srinivasa Ramisetti wrote: I think the minimum coordinates are (0,0,0) Not really. GROMACS will accept negative coordinates and then re-wrap them into the periodic box with its origin at (0,0,0). An actual error message and full command from the OP would be helpful

Re: [gmx-users] Regarding minimum size

I think the minimum coordinates are (0,0,0) Srinivasa On 12/03/2018 18:01, Chhavi Yadav wrote: Hi Justin, Thanks for the reply. I meant this : In our application, we need to randomly sample coordinates for atoms. When we were doing that, we got an error message for one of the random coordinate

Re: [gmx-users] Regarding minimum size

Hi Justin, Thanks for the reply. I meant this : In our application, we need to randomly sample coordinates for atoms. When we were doing that, we got an error message for one of the random coordinate samples because the sample coordinate was smaller than the minimum coordinates. What is this

Re: [gmx-users] Regarding minimum size

On 3/12/18 1:30 PM, Chhavi Yadav wrote: Hello, This is regarding the minimum size or resolution used in gromacs for sampling coordinates of atoms. I know that the maximum size is the matrix box. Can someone please let me know what the minimum is? I'm not sure if this is the answer to your