Hi all,
I was trying to pass a file through GROMACS using following command:
$gmx grompp -f minim_gmx5.mdp -c Solv.gro -p topol.top -o ions.tpr
Then the follwing error popped up:
Atomtype sy not found
This is due to the presence of sulphur atom in my drug molecule
Zafirlukast. I us
Hi all,
I was trying to pass a file through GROMACS using following command:
$gmx grompp -f minim_gmx5.mdp -c Solv.gro -p topol.top -o ions.tpr
Then the follwing error popped up:
Atomtype sy not found
This is due to the presence of sulphur atom in my drug molecule
Zafirlukast. I us
Hi all,
The force field combination used in GROMOS96 53A6 with extended Berger
lipids contains L-J interaction cross-terms between protein lipid atom
types? If so how abnormally high L-J interactions are tackled?
In my case, to prepare the topology of my system (which contains proteins
and DPPC),
Hi,
There's also atomtypes.atp file in force fields that perhaps you need to
adjust.
Mark
On Tue, Feb 13, 2018 at 10:40 AM wrote:
>
> Hi all,
>
>I was trying to pass a file through GROMACS using following command:
>
> > $gmx grompp -f minim_gmx5.mdp -c Solv.gro -p topol.top -o ions.tpr
>
>
Hi,
I am trying to simulate a system in which a protein will be pulled from a
distance and ultimately be put on a DPPC membrane system. I went through
Lemkul's tutorial on membrane and successfully simulated protein-membrane
systems before.
In this case, I put the protein in the required coordina
Hi Szilard
Thank you for answering. It did indeed show a significant improvement
with, in particular,
$ gmx mdrun -v -deffnm md -pme gpu -nb gpu -ntmpi 8 -ntomp 6 -npme 1
-gputasks 0001
I also now understand better how to control each individual
simulation. Your point on maximizing aggregate
> On 12. Feb 2018, at 22:44, Daniel Kozuch wrote:
>
> Carsten,
>
> I was hoping yo use tune_pme to optimize a REMD job across multiple nodes,
> so I think I need it compiled with MPI (please let me know if that logic is
> incorrect).
Strictly speaking, tune_pme is a serial program that calls M
Hi
I want to obtain shear viscosity for ionic mixtures. I use the method Berk
Hess gives in his paper, (J. Chem. Phy *116*, 209 (2002)).
I would like to know if this is a better method, or the
muller-plathe method (Phy. rev. E *59*, 5 (1999))?
Best regards
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Suppose the trajectory of molecular system with interactions between all
molecules. How is to obtain the time dependence of intramolecular energy of the
given molecule with unique resname and the total energy of this molecule in the
system including intermolecular interactions?
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Gromacs Users
Dear All,
Is there any way to calculate the change in shape of a protein with respect
to simulation time using GROMACS or VMD? By the use of the word 'shape', I
mean to say 'spherical' or 'elliptical'; or more specifically the value of
eccentricity of the protein wrt simulation time.
My guess is
You can calculate the asphericity, for example. You just need the
components of the gyration tensor which are given by gmx polystat, if my
memory serves me right.
There are several papers about this. A quick search on Google scholar will
surely produce results.
I would link the papers or the form
Just a quick update here regarding regression tests. On an old machine with
a single puny GTX 960, the 2018 build passes all tests with
Start 9: GpuUtilsUnitTests
9/39 Test #9: GpuUtilsUnitTests Passed5.64 sec
Hope this is useful.
Alex
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