On 7/28/17 2:54 PM, Mohammad Zahidul Hossain Khan wrote:
Dear User
I have protein-ligand system. I have basic idea for energy minimization.mdp
parameter.
;
integrator = steep
emtol = 10.0
emstep = 0.01
nsteps = 500
energygrps = Protein OAI
;
nstlist= 1
cutoff-scheme = Verlet
ns_type=
Hi All,
Does anyone have the itp file for TIP4P-D water (J. Phys. Chem. B, 2015, 119
(16), pp 5113–5123) and also the parameters that are needed to be added to the
ffnonbonded.itp file for this water model?
ThanksAtanu
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In case anyone is interested, here is a copy of the script I am currently
using to interface Gromacs 2016.1 with Gaussian 09 without altering the
source code of Gaussian 09. It is based on Gerrit Groenhoef's script,
available at wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian, with some
alterations so
Dear User
I have protein-ligand system. I have basic idea for energy minimization.mdp
parameter.
;
integrator = steep
emtol = 10.0
emstep = 0.01
nsteps = 500
energygrps = Protein OAI
;
nstlist= 1
cutoff-scheme = Verlet
ns_type= grid
rlist= 1.0
coulombtype= PME
rcoulomb= 1.0
Hi,
The QM/MM code is essentially untested and unmaintained and wasn't
developed for that version of GAUSSIAN, so you're dicing with death. Death
looks like he's rolling well. ;-) I recommend using either the exact
software versions used in published work, or some other package.
Mark
On Fri, 28
Hi,
On Fri, 28 Jul 2017 17:49 Atila Petrosian wrote:
> Dear gromacs users,
>
> I had done a md simulation for 100 ns. I continued that for another 50 ns.
>
> gmx grompp -f 100.mdp -c eq.gro -p system.top -o 100.tpr -n index.ndx
> gmx mdrun -nb gpu -v -deffnm 100
>
>
No, I haven't been changing the code. I have been doing mixed qm/mm (using
Gaussian 09 for the qm calculations) with some frozen atoms in the qm
region. There were two changes I made to this run that altered it from
previously successful runs: I increased the time step slightly, and I added
a
Dear gromacs users,
I had done a md simulation for 100 ns. I continued that for another 50 ns.
gmx grompp -f 100.mdp -c eq.gro -p system.top -o 100.tpr -n index.ndx
gmx mdrun -nb gpu -v -deffnm 100
gmx grompp -f 50.mdp -c 100.gro -p system.top -o 50.tpr -n index.ndx
gmx mdrun -nb gpu -v -deffnm
Dear GROMACS Users,
I am interesting in the work-flow of the shear flow modeling in GROMACS.
I am dealing with a complex MARTINI CG membrane system consisted of several
proteins embedded within big POPC-cholesterol bi-layer solvated in
non-polarizable water. Within this system I would like to
Dear Gromacs community,
I am attemping to use Gromacs for a Coarse - grained simulation. In our
model, we have a term similar to the angle harmonic potential term, but the
variable is not angle but the volume created by three consecutive vectors.
I don't know if there is a way to implement that
Dear Gromacs community,
In the [ atomtypes ] directive, according to Gromacs manual, it should have
7 seperated fields, which are name, at.num, mass, charge, ptype, c6, c12.
However, when I remove the field of at.num, Gromacs still works without
notifying any error. If I insert 2 fields more, it
Thank you for explaining.
Best wishes,
Dawid
2017-07-28 15:11 GMT+02:00 Mark Abraham :
> Hi,
>
> Seems like the extremes of normal variation of unconstrained bonds. As gmx
> help check suggests, the feature exists as a quick sanity check. The use of
> "correct" is in
Hi,
Seems like the extremes of normal variation of unconstrained bonds. As gmx
help check suggests, the feature exists as a quick sanity check. The use of
"correct" is in the sense of "between sensible atom indices" rather than
suggesting that only one length is valid.
Mark
On Fri, 28 Jul 2017
Hi,
No, those bonds I get the message were not constrained and virtually in
every frame there is different
bunch of bonds for which I get this message. Because the whole output from
gmx check is 1.1 GB,
I just give you a few examples.
Reading frame 0 time0.000
# Atoms 24884
Precision
Hi,
It's hard to tell without seeing the messages and knowing whether those
bonds were constrained.
Mark
On Fri, 28 Jul 2017 13:19 Dawid das wrote:
> Dear Gromacs Users,
>
> I get a bunch of communicates when I run
> gmx check -f npt-md2.xtc -s1 npt-md2.tpr >&
Dear Gromacs Users,
I get a bunch of communicates when I run
gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out
saying that I get different bond lengths than they should be. Can that be
caused by only 0.001 nm precision of my results?
Also I am not exactly sure if I understand correctly
Hello,
You can also set the variable of GMXLIB so that pdb2gmx can find the
force field you want to use, like:
GMXLIB=/ path /charmm36m.ff
Best,
Qinghua
On 07/28/2017 10:53 AM, Souparno Adhikary wrote:
Hi,
I want to use the latest CHARMM36m force field which I downloaded from
MacKerell
On 28/07/17 10:53, Souparno Adhikary wrote:
Hi,
I want to use the latest CHARMM36m force field which I downloaded from
MacKerell group's website. I use a common HPC system and do not have an
administrator account.
Can you give me an idea how I can add this forcefield to the pdb2gmx
options? We
Hi,
On Fri, 28 Jul 2017 10:53 Souparno Adhikary wrote:
> Hi,
>
> I want to use the latest CHARMM36m force field which I downloaded from
> MacKerell group's website. I use a common HPC system and do not have an
> administrator account.
>
> Can you give me an idea how I can
Hi,
On Fri, 28 Jul 2017 10:37 leila karami wrote:
> Dear gromacs users,
>
> I am running CG MD simulation on a Rocks cluster using the following
> command:
>
> gmx_mpi mdrun -nb gpu -v -deffnm gpu_md -ntomp 16 -gpu_id 0>& md.job &
>
> I tried the different value for the
Hi,
I want to use the latest CHARMM36m force field which I downloaded from
MacKerell group's website. I use a common HPC system and do not have an
administrator account.
Can you give me an idea how I can add this forcefield to the pdb2gmx
options? We are using quite an old version of GROMACS-
Dear gromacs users,
I am running CG MD simulation on a Rocks cluster using the following
command:
gmx_mpi mdrun -nb gpu -v -deffnm gpu_md -ntomp 16 -gpu_id 0>& md.job &
I tried the different value for the -ntomp option. With -ntomp 16 run
will finish sooner than the other values for -ntomp.
In
You might find this reference handy - it has a really nice explanation for how
to look
at a log file
Topology preparation, "What's in a log file", basic performance improvements:
Mark Abraham, Session 1A
Hi,
Your xtc file has only the group you wrote, so it isn't valid to index into
it with an index file that was made for a conformation with many other
atoms. That's the mismatch the message mentions. For your xtc, "System" is
the subset of *it* that you seem to want for your analysis. Note that
Hi,
That's a new one for me ;-) So new that I assume you were changing the code?
Mark
On Fri, 28 Jul 2017 00:51 Clinton King wrote:
> Has anybody ever seen the following error message before?
>
>
> Program: gmx mdrun, version 2016.1
> Source file:
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