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
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
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
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
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
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
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
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
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
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 next.
I get the c
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
wrote:
>
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 main(int argc, char *arg
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
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 = mdrunner.globalState.get()
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 her
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
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 minim
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 qu
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