Dear gmx users,
I know this is a old topic. I searched the mailing list however haven't find a
answer.
I am calculating the solvation free energy of a small ligand in water, using
FEP theory. Two steps are applied: firstly decrease the atomic charge to zero;
secondly decrease the VDW to zero.
ubject: Re: [gmx-users] The solvation free energy of a vdw ligand
> To: "Discussion list for GROMACS users"
> Date: Friday, February 17, 2012, 2:37 PM
>
>
> Tanping Li wrote:
> > Hey Justin,
> >
> > Thanks for the help. There is a ligand in my system,
&
. Thanks again and have a
good weekend!
Tanping
--- On Fri, 2/17/12, Justin A. Lemkul wrote:
> From: Justin A. Lemkul
> Subject: Re: [gmx-users] The solvation free energy of a vdw ligand
> To: "Discussion list for GROMACS users"
> Date: Friday, February 17, 2012, 1:38
al, but haven't find that.
Tanping
--- On Fri, 2/17/12, Justin A. Lemkul wrote:
> From: Justin A. Lemkul
> Subject: Re: [gmx-users] The solvation free energy of a vdw ligand
> To: "Discussion list for GROMACS users"
> Date: Friday, February 17, 2012, 10:14
a lot but haven't find the reason.
Yours
Tanping
--- On Thu, 2/16/12, Tanping Li wrote:
> From: Tanping Li
> Subject: [gmx-users] The free energy of vdw part
> To: gmx-users@gromacs.org
> Date: Thursday, February 16, 2012, 11:28 AM
> Dear gmx users,
>
> I am
Dear gmx users,
I am calculating the free energy of solvating a small ligand by water, using
FEP method. The free energy is separated into the contribution of electric+vdw.
I find problem for the vdw part.
I am using gromacs-3.3.1. In the top file, I set the state B of ligand where LJ
paramete
Dear gromacs users,
I am a gromacs user, and I am calculating the binding free energy between
protein and ligand. A package "sietraj" looks very tempted, which is an
alternative of MM-PBSA. However, the prmtop (topology) and trajectory in amber
is required.
It is easy to convert gromacs trr to
distance constraint.
>
> On 11/7/2007 5:11 AM, Tanping Li wrote:
> > Dear all,
> >
> > I searched the mailling list, and still can't find
> a
> > way to set up my system: a ligand covalently bond
> to
> > protein.
> >
> > I don't know if ther
Dear all,
I searched the mailling list, and still can't find a
way to set up my system: a ligand covalently bond to
protein.
I don't know if there is a easier way to do this. What
I can think of is:
1) Add a bond I like in the specbond.dat file;
2) Add a block for ligand in the rtp file;
3) run
>
>
> >Date: Sun, 7 Oct 2007 08:46:04 -0700 (PDT)
> >From: Tanping Li <[EMAIL PROTECTED]>
> >Subject: Re: [gmx-users] Different nstxout and
> nstvout in mdp file
> > gives totally different trajectory
> >To: Discussion list for GROMACS users
>
.
Yours
Tanping
--- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
> Hi Tanping Li,
>
> Can you be more elaborate? What are the differences?
> What do you mean with
> "totally different"? Did you run it on the same
> machine? Was everything else
> the same?
cases). I am really
confused: nstxou JUST sets the frequency to output the
coordinate, why I get different results? Looking
forward to your opinion and thanks a lot.
Yours
Tanping Li
___
gmx-users mailing listgmx-users@gromacs.org
http
Dear all,
I am testing the INM analysis. I get the eigenvector
file eigenvector.trr; and then do the projection on
INM normal modes by the command:
g_anaeig -proj -v eigenvector.trr -f c.gro -proj
proj.xvg
But what I get from proj.xvg is pretty stange. Except
the first few values, all of t
Dear all,
I am doing the INM analysis. I get the eigenvector
file eigenvector.trr. According to my understanding, I
can get the corrdinates of the system based on those
INM modes by the command:
g_anaeig -proj -v eigenvector.trr -proj proj.xvg
But what I get from proj.xvg is pretty stange. Exce
Dear all,
I am trying to do the INM analysis for a small system:
one residue Trp in water. Before I do the g_nmeig, I
need to minimize the whole structure use em. Should I
minimize tbe whole system, or ONLY the protein
conformation in vacuum, as I see some people did in
mailing list? Since I find
Dear all,
Is there a way to get the eigenvalue of a subgroup in
the Hessian? For example, I want to get the frenquency
between a specific residue and water; but what I
directly get from g_nmeig is the eigenvalue of the
whole space matrix.
I checked the mailing list, but can't find a way. I
hope
ok to see what
> they've done and
> whether it worked well. I am not too clear on why
> you would want to do
> this.
>
> David
>
> >
> >
> > Tanping
> >
> >
> >
> > --- David Mobley <[EMAIL PROTECTED]> wrote:
> >
> &g
your nice help.
Tanping
--- David Mobley <[EMAIL PROTECTED]> wrote:
> What are you trying to use orientational restraints
> to restrain?
> Ordinarily, you probably don't want such restraints,
> hence the default
> value is zero.
>
> On 7/25/06, Tanping Li
Hellow everyone,
I notice that the default value for orire_fc=0, which
set the orientation restrain as the none. What is the
reasonable value for the orire_fc? Any suggestion will
be greatly appretiated. Thanks a lot!
Best
Tanping
___
gmx-users mailing
Dear all,
I plan to run solvate a small molecule using Gromacs.
This small molecule is not a protein or DNA or RNA. So
I meet the problem at the first step to run pdb2gmx,
the wrong information says Gromacs can't recognize
this molecule.
Is there a way to assign charge to this small molecule
and g
Dear David,
Thank you so much for the reply. I used the pme,
cutoff for rvdw =1.4, rlist=rcoulomb=0.9, so that is
not supposed to give me the same rotational relaxation
time for SPC/E as 3.8ps in your paper?
Best
Tanping
--- David van der Spoel <[EMAIL PROTECTED]> wrote:
> Tanping
Dear all,
I simulated a box of pure water usin NPT. I use gmx96
force field and standard mdp file for the gmx96 force
field. The time scale of dipole correlation function
is 2.8ps, which is different from David's result 3.8ps
in the JCP paper. Is this 3.8ps sensitive to the mdp
file or the force f
22 matches
Mail list logo
