I found the problem finally. It had to do with the fact that my charge groups
contained atoms in different residue. I just defined one charge group for
every atom, and everything worked.
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Dear list members,
I am trying to simulate an infinite layer of quartz in Gromacs. Due to my
needs (afterwards I need to place a large molecule on top of it) the surface
must be at least 12x12 nm^2. I generated the input files from a pdb file of
the structure, and adapted the OPLS force field to m
I received this answer:
Mark Abraham Mon, 03 Jun 2013 08:02:56 -0700
That looks like there's a PGI compiler getting used at some point (perhaps
the internal FFTW build is picking up the CC environment var? I forget how
that gets its compiler!). If you do find * -name config.log then perhaps
you c
Hello all,
I have a very similar problem, but compiling both Gromacs 4.6 and 4.6.1 with
cmake and MPI support (no problems with non-MPI installation). I have cmake
version 2.8.7, openmpi version 1.4.1, and I am using gcc version 4.6.3 in a
linux Ubuntu 4.6.3. I use the cmake options:
cmake -DGMX_
Hello all,
I am afraid that, after reading all the documentation I could find about
Coul-SR and LJ-SR, I still do not understand what these terms account for.
I am running a simulation of one single polymer chain in water. My values
for cut-off radious are rlist=rcoulomb=rvdw=1.5, I am using PME
Thank you!
That clarifies it, I will redefine the residues. This definition was good
enough for an all-atom force field, but it seems that not for this.
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Sent from the GROMACS
Thank you Justin, but there is still something I do not understand. Could you
please help me with it?
I believe that with the line
-CB CA1 +CB +CA1 gd_34
in aminoacids.rtp I am defining the torsion the program is complaining
about. I also tried with a line
-CH3 CH1 +CH2 +CH1 gd_34
Hello all,
I have the same problem, but I think the dihedral is properly defined.
I am running a polymer with the G53A6 force field. First I use pdb2gmx to
generate a conf and a top file. When I run grompp, I have the error(s):
ERROR 1 [file topol.top, line 1507]:
No default Proper Dih. types
Yes, that seems to be the problem. I minimized the configuration using
Conjugated Gradient and everything looks right now.
Thank you again!
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Sent fro
I do have constraints, all the bond lengths are fixed and they are specified
in the topology file. Am I doing something wrong? I copy here the definition
of one of the models I use. I also tried using in the input the line:
constraints = all-bonds
instead of
constraints
Thanks for the tip about nstlist, I will make good use of it.
I also tried the NPT and the NVT ensembles with different temperatures and
pressures, and I always had blow-up and large energies. Now I tried
decreasing the time step up to 10 times, but still have blow-up problem and
the potential en
This is my mdp file for energy minimization:
constraints = none
; integration parameters
integrator = l-bfgs
dt = 0.00
nsteps= 15000
; center of mass removal
nstcomm = 10
comm_mode = Linear
; ne
Thank you,
At the end the problem was solved just increasing the time coupling constant
of the barostat tau_p. The original value of 0.15 that I set at the
beginning was too small, with 0.5 works fine.
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