Dear Users !
I have done a minimization for a tetrapeptide in a water box
with conjugate gradient minimization of 1000 steps
when I convert it to pdb as below
trjconv -f em.trr -o min.pdb -s em.tpr << EOF
0
EOF
the out put pdb has many structures
as follo
Dear Users !
I have done a minimization for a tetrapeptide in a water box
with conjugate gradient minimization of 1000 steps
when I convert it to pdb as below
trjconv -f em.trr -o min.pdb -s em.tpr << EOF
0
EOF
the out put pdb has many structures
as follo
Dear Users
I have a peptide, (1AKI.pdb)
My aim is to solvate it in the presence of the explicit water molecules
and do minimization and to split the energy terms , and to see the energy
contribution from each terms
for this i have done the following in gromacs
-
On 17/12/2011 5:25 PM, balaji nagarajan wrote:
Dear Users !
I have used the energy group option to split the energy terms ,
for the protein and the water.
You have split the *non-bonded* terms
Dear Users !
I have used the energy group option to split the energy terms , for the protein
and the water.
It gives all the terms ,
protein-protein , water-water , water-protein .
I have a doubt ,
the distance and the angle are taken for both water and the protein ,
how one can get the
Dear Users !
I have minimized the attached file using the gromacs43a1 and oplsaa force field
using spc water molecules
I have used the following script for generating topology .
i minimized for 2000 steps , my doubt is when i rewrite the minimized pdb , in
case of oplsaa
i was able to get
:02:04 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] error_in topology
>
>
>
> balaji nagarajan wrote:
> > Dear Users !
> >
> > I have a problem in generating the topology of the attached molecule as pdb.
> >
Dear Users !
I have a problem in generating the topology of the attached molecule as pdb.
earlier i have done using the same pdb for solvating the structure using spc
and spce water box ,
there was no such error when i do for TIP4P and oplsaa force field i got the
error
as follows
-
Dear Users !
Is it possible to calculate the free energy for a molecule ,
at the zero step MD , when i see the mail list this question has been posted
once ,
but i could not find the reply for this !
is there any option for this like g_energy !
Dear Users !
I have a doubt in minimizing the structure with water box !
I have taken a penta peptide and solvated it with spce water box !
I have minimized the system with the minim.mdp file which i have attached ! ( i
have used steep option )
when I calculated the protein- protein and
Dear Users !
I have a problem in taking the inter and intra molecular interaction energy
from a pdb , which is being minimized by minim.mdp !
when i use the
g_energy -f *.edr it gives the list of all possible interaction energy as
average value , but i want it only for the minimized f
Dear Users !
I have done the g_energy using the *.edr file !
In that it prints all the energy terms , i can understand most of the terms !
i dont know what does Mu-X , Mu-Y , Mu-Z represents and its importance !
I would like to know the detail of the force fields included in the gromacs !
ct: Re: [gmx-users] interaction energy
>
>
>
> balaji nagarajan wrote:
> >
> >
> >
> > Dear Users !
> >
> > i would like to do this to a set of files !
> > so how to print the required values in the text mode or is there any
> > fla
ct: Re: [gmx-users] interaction energy
>
>
>
> balaji nagarajan wrote:
> > Dear Users !
> >
> > Now i am able to do the protein solvent interaction !
> >
> > thanks ! i have understood !
> >
> > when i used the energygrps ,
> > wh
Dear Users !
Now i am able to do the protein solvent interaction !
thanks ! i have understood !
when i used the energygrps ,
when i used the
g_energy -f em.edr
this command it prints all terms and asks to make selection as below,
1 Bond 2 Angle3 Proper-Dih.
Thanks for the reply !
I have tried building the topology with generating the index file
make_ndx -f *
it gave options i have selected the protein and the solvent
then i gave minimization
in the minimization file i have included
energygrps = Protein SOL ,
but the energy file ha
Dear Users !
I have took a penta peptide and did topology generation ,
I have solvated it with water box ,
now i did a minimization with zero step , to know the energy of the initial
molecule ,
i used g_energy for the out put ,
like
$ g_energy -f em.edr
it gives as follows , i have to
Dear Users !
i have tried in generating the -ter option in generating the topology file !
it asks the below if i give the ter option ,
Select start terminus type for TYR-1
0: NH3+
1: ZWITTERION_NH3+
2: NH2
3: None
then if i give option 1 it chooses ZWITTERION_NH3+ , i want to make the
Dear users !
I am new to gromacs !
I have installed the package ! and it is working fine !
I tried to solvate a peptide and i was able to select the force field of my
interest ,
I would like to calculate the energy of the structure in terms of inter and
intra and i want to
print all th
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