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Dear all,
I am calculating the mutation free energies using TI method for a small
globulin protein which contains about 40 residues.
I meet convergence problems in the FE calculations:
(1) when simulations start with different velocities for the some lambda
points, the variance of dGdlamba is big
Dear all,
Does Gmx provide the functions to decompose the free energy calculated
using TI into various components, such as electrostatic, VDW, covalent
or contribution from each residue?
If it has, where can I find the procedures to do it?
thanks a lot
Qiang
_
thank you for the rational explanation.
but is the free energy change in the charge on/off step(~10kJ/mol) small
enough to ignore the flucturations? The free energy change in the LJ
mutation step is about 8kJ/mol.
On Fri, Jan 16, 2009 at 11:56 PM, Jochen Hub wrote:
> friendli wrote:
>
Dear all,
When I performing mutation free energy calculation from Leu to Ala, I
first turn off the charge on the side chain of Leu. As I read from the
GMX archive, the dG/dl curve should be rather smooth for turning off the
partial charge.
In this step(charge off/on), however, I can not obtai
cs.org
> > > > Subject: Re: [gmx-users] OPLSAA parameters
> > > >
> > > > Thanks Mark.
> > > >
> > > > Hope the developers can consider to output the parameters into .top
> > > file
> > > > explicitly. That would be helpful for mutation calcula
I think I have found the answer by adding " flags = flags | TRX_READ_V |
TRX_READ_F ;".
thanks to all.
On Sat, Nov 29, 2008 at 12:53 PM, friendli <[EMAIL PROTECTED]> wrote:
> I have checked with gmxcheck and velocities and forces are output in .trr.
> I am playing temp
ource of g_traj or trjconv
> for examples.
>
> Cheers,
>
> Tsjerk
>
> On Fri, Nov 28, 2008 at 10:33 AM, Mark Abraham <[EMAIL PROTECTED]>
> wrote:
> > friendli wrote:
> >>
> >> Dear all users,
> >>
> >> A silly question:
Dear all users,
A silly question:
I want to print out the velocities and forces in the trajectories using
template.c.
In template.c, the coordinates of atom n is in fr.x[n][XX].
Reading the trx.h, i see the x,v and f are defined in the same way. So I
just change it to fr.v[n][XX] for velocit
; > > To: gmx-users@gromacs.org
> > > Subject: Re: [gmx-users] OPLSAA parameters
> > >
> > > Thanks Mark.
> > >
> > > Hope the developers can consider to output the parameters into .top
> > file
> > > explicitly. That would be helpful for
ECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] OPLSAA parameters
>
> Thanks Mark.
>
> Hope the developers can consider to output the parameters into .top
file
> explicitly. That would be helpful for mutation calculations at least, I
> think.
>
>
>
Thanks Mark.
Hope the developers can consider to output the parameters into .top file
explicitly. That would be helpful for mutation calculations at least, I
think.
Mark Abraham wrote:
friendli wrote:
Hi Mark,
the atom types in .top file is opls_???, but the atom types(or
"name
Hi Mark,
the atom types in .top file is opls_???, but the atom types(or "name")
in [bondtypes] in ffoplsaabon.itp file is C, H, CT, C_3, etc.
So we still need to look up ffoplsaanb.itp to link these two "atom type"
(or "name"), right?
thanks
Qiang
Mark
I look at the .top file generated by grompp (-pp).
However, for me it is more like a copy of all the force field files
into one .top file, so the content are the same as individual ones.
Do I miss anything?
Thank you
Qiang
Justin A. Lemkul wrote:
friendli wrote:
Thank you Justin.
Can
Is that right? why it comes to such complex in GMX?
thanks
Qiang
Mark Abraham wrote:
friendli wrote:
In ffoplsaa.rtp, I find atom name CG and OG1 corresponds to atom type
opls_235 and opls_236.
While in oplsaanb.itp, the atom type opls_235 and opls_236
corresponds to atom "name"(as
me atom? what is the
difference?
Qiang
Justin A. Lemkul wrote:
friendli wrote:
Thank you Justin.
Can you tell me how i can find the link between atom names and atom
types?
That is listed in the .rtp:
; name typechargecgnr
CGopls_2350.500 3
The thing I wanna
[ASN] in ffoplsaa.rtp?
thanks
Qiang
Justin A. Lemkul wrote:
friendli wrote:
Dear all,
To understand the exact parameters used in oplsaa force field, I read
the ffoplsaa*.*** files.
But I can not find all the corresponding atom types in the
ffoplsaa.rtp and ffoplsaabon.itp files.
for
Dear all,
To understand the exact parameters used in oplsaa force field, I read
the ffoplsaa*.*** files.
But I can not find all the corresponding atom types in the ffoplsaa.rtp
and ffoplsaabon.itp files.
for example, in rtp file, there is a bond between atom type CG and OG1.
But in *bon.itp,
Dear all,
Are the topology components of OPLSAA force field explicitly displayed
in Gromacs 4.0?
I mean the bond, angle, dihedral types(or parameters) following the
composed atoms. They are not showed in .top file when oplsaa FF is used,
not like other force field, e.g. Gromos96.
thanks
Qia
atoms that you are going to modify.
David
On Fri, Sep 26, 2008 at 2:14 AM, friendli <[EMAIL PROTECTED]> wrote:
Dear all,
I have a mutation free energy calculation from D(asp) to E(glu). The charge
is not changed for the overall mutation. However, following Dr. David
Molbey&
e
CH2 groups? You only have to mind perturbing the bonding and such in
the right way then.
Cheers,
Tsjerk
On Sat, Sep 27, 2008 at 6:32 PM, friendli <[EMAIL PROTECTED]> wrote:
Dear all,
I have a mutation free energy calculation from D(asp) to E(glu). The charge
is not changed for
Dear all,
I have a mutation free energy calculation from D(asp) to E(glu). The charge
is not changed for the overall mutation. However, following Dr. David
Mobley's suggetion, electrostatic and VDW interaction should be modified
separately, so in the first step we need to turn off the charge from
Dear all,
I have a mutation free energy calculation from D(asp) to E(glu). The charge
is not changed for the overall mutation. However, following Dr. David
Mobley's suggetion, electrostatic and VDW interaction should be modified
separately, so in the first step we need to turn off the charge from
Dear all,
I have a mutation free energy calculation from D(asp) to E(glu). The
charge is not changed for the overall mutation. However, following Dr.
David Molbey's suggesion, electrostatic and VDW interaction should be
modified separately, so in the first step we need to turn off the charge
Hi,
I use thermodynamics integration.
The protocol is 1000step energy minimization, 20 ps bond-constraint MD,
and then 200ps MD for collecting dgdl.
thanks
Qiang
Gerrit Groenhof wrote:
Looks like hysteresis. Do you do slow growth, or discrete FEP?
Gerrit
Dear all Gmxers,
I am calcula
Dear all,
I am calculating FE using TI. I have a question about mutating existing
atoms with different mass.
for example, using ffG53a6 force field, in one case i need to mutate CH2
to CH3,
should I use
[ atoms ]
17CH3 2ALA CB 6 0 15.035
CH20
Dear all,
I am calculating FE using TI. I have a question about mutating existing
atoms with different mass.
for example, using ffG53a6 force field, in one case i need to mutate CH2
to CH3,
should I use
[ atoms ]
17CH3 2ALA CB 6 0 15.035
CH20
Dear all,
I am calculating FE using TI. I have a question about mutating existing
atoms with different mass.
for example, using ffG53a6 force field, in one case i need to mutate CH2
to CH3,
should I use
[ atoms ]
17CH3 2ALA CB 6 0 15.035
CH20
Dear Gmx users,
I am calculating the mutation free energy from amino acid Asp to Asn as
a test job for my practice.
I have some questions about setting up the topology file.
1, from Asp to Asn mutation, the -CH2-COOH changes to -CH2-CO-NH2 or
simply -OH to -NH2.
In topology, O <-> N.
What ab
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