Dear Prof.
I have several questions about trjconv, please help me.
In my simulation is created 2 micelles.
1- When I do 3 steps of micelle clustering as follows:
a- trjconv -f md.xtc -o a_cluster.gro-e 60 -pbc cluster
b- grompp -f md.mdp -c a_cluster.gro -o a_cluster.tpr
c- trjconv -f
Hello
after use of grompp I got the following errors:
ERROR 1 [file topol.top, line 172]:
No default Angle types
this error repeats
ERROR 38 [file topol.top, line 233]:
No default Improper Dih. types
this error repeats also
Excluding 3 bonded neighbours molecule type 'Isoalloxazin'
Hi,
We have run an NPT equilibration on a protein embedded in a membrane and
calculated the average pressure using g_energy. We then imported the resulting
xvg file into excel and recalculated the average. The 2 numbers differed.
Specifically, the gromacs average pressure was 0.942858 while
On 12/26/2011 10:43 PM, Efrat Exlrod wrote:
Hi,
We have run an NPT equilibration on a protein embedded in a membrane
and calculated the average pressure using g_energy. We then imported
the resulting xvg file into excel and recalculated the average. The 2
numbers differed. Specifically, the
On 12/26/2011 8:22 PM, Lara Bunte wrote:
Hello
after use of grompp I got the following errors:
ERROR 1 [file topol.top, line 172]:
No default Angle types
grompp needs either parameters for the angle interaction on the line it
is defined, or one able to be looked up from the [angletypes]
On 12/26/2011 7:53 PM, mohammad agha wrote:
Dear Prof.
I have several questions about trjconv, please help me.
In my simulation is created 2 micelles.
1- When I do 3 steps of micelle clustering as follows:
a- |trjconv -f md.xtc -o a_cluster.gro-e 60 -pbc cluster|
| b- ||grompp -f md.mdp
Hello all,
For some time now I have been unable to find a solution to my problem. I am
attempting to do umbrella sampling on a protein ligand system. To generate the
starting configurations, I use the following mdp file:
title = Protein-ligand complex MD Simulation
define =
Eric LeGresley wrote:
Hello all,
For some time now I have been unable to find a solution to my problem. I am
attempting to do umbrella sampling on a protein ligand system. To generate the
starting configurations, I use the following mdp file:
title = Protein-ligand complex MD
On 12/25/2011 9:44 PM, ?? wrote:
Dear teacher,
how to use gromacs 4.5.5's temple?
I expect that it is not meant to be functional. It's meant to be a
template from which you can write functional code without having to work
too hard on making it work like GROMACS tools work.
Mark
i make
On 12/25/2011 7:56 PM, Ashalatha Sreshty wrote:
Dear All,
I have a problem running gromacs for a oligosaccharide. it has 14
units sugars containing glucose, mannose and N-acetyl glucosamine
units. I want to do MD simulations for this with opls aa force field.
For this I have generated the .itp
Dear all,
I am trying to create tmao box.Energy minimization, simulated annealing
(Cooling under
high pressure and again heating at normal pressure) as well as final
equilibration ran smoothly.
But finally I got a box where all water molecules got accumulated in two
three small region within the
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