Re: [gmx-users] Constant pH replica exchange MD in Gromacs (Muneeswaran S)

[Muneeswaran S]

Thanks for your information.

On Wed, 18 Dec 2019 at 12:30, Groenhof, Gerrit  wrote:

> No, but this is possible in Charmm and in Amber.
> Best,
> Gerrit
>
>
>
> > Date: Wed, 18 Dec 2019 11:52:15 +0530
> > From: Muneeswaran S 
> > To: gmx-us...@gromacs.org
> > Subject: [gmx-users] Constant pH replica exchange MD in Gromacs
> > Message-ID:
> >apdmp_+baoplz5rc3g8...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Good Morning Friends,
> >
> >   I want to run Constant pH replica exchange MD
> > for my peptides. Is that possible with GROMACS?
> >
> > please let me know. Its urgent.
> >
> >
>
>
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[gmx-users] Constant pH replica exchange MD in Gromacs

[Muneeswaran S]

Good Morning Friends,

   I want to run Constant pH replica exchange MD
for my peptides. Is that possible with GROMACS?

please let me know. Its urgent.
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[gmx-users] Generating Ramachandran Plot monitoring movie.

[Muneeswaran S]

Good Evening Friends,

I had some problem with my MD analysis. I want to
monitor the Ramachandran plot of some residues.

My problem let say I had a tri peptide from which we can get 4 dihedral
angles and we can only plot the ramachandran plot for the Mid residue that
is second residue. Here What I want is some script or Method to monitor the
changes occur in the Ramachandran plot during the simulation period.  Let
say I have 1000 saved frames each frame has it own Ramachandran plot I want
like 40 sec or less duration movie or of the Ramachandran plot from frame 1
to 1000. Them I can monitor the the path in which the peptide secondary
structures changes from the frame 1 to 1000.

 Thank You.
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[gmx-users] Gromacs error while running energy minimization step

[Muneeswaran S]

I got the following error while running the gromacs

























*NOTE: disabling dynamic load balancing as it is only supported with
dynamics, not with integrator 'steep'.Using 16 MPI threadsUsing 4 OpenMP
threads per tMPI threadOn host localhost.localdomain 2 GPUs auto-selected
for this run.Mapping of GPU IDs to the 16 GPU tasks in the 16 ranks on this
node:
PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1---Program:
gmx mdrun, version 2018.6Source file: src/gromacs/utility/filestream.cpp
(line 115)Function:gmx::internal::FileStreamImpl::FileStreamImpl(const
char*, const char*)MPI rank:12 (out of 16)System I/O error:Failed to
compile NBNXN kernels for GPU #Quadro P620  Could not open file
'/usr/share/gromacs/opencl/nbnxn_ocl_kernels.cl
'Reason: No such file or directory
(call to fopen() returned error code 2)For more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
*
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